Genome Assembly workshop

Software List

• Velvet 

Current version 1.2.10

Source code in C language

https://www.ebi.ac.uk/~zerbino/velvet/

• VelvetOptimiser 

Current version 2.2.5

Perl script

Requirements

•   Velvet >= 0.7.51 (including 1.x series)  : Velvet 1.2.10

•   Perl >= 5.8 

•   BioPerl >= 1.4 

http://www.vicbioinformatics.com/software.velvetoptimiser.shtml

• SPAdes 

Current version 3.12

Executable files (Linux 64 bits and MacOSx) and Source code

http://cab.spbu.ru/software/spades/

• MaSuRCA 

Current version 3.2.8

 Source code in C language

 https://github.com/alekseyzimin/masurca

Raw data

Use a part of Chr11 of Solanum lycopersicum (Tomato)
Chr11 ~53 Mbp -> ~ 4.8 Mbp
       Generate simulated illumina Paired-end FASTQ files
  • 151 bp paired-end reads
  • Insertion length 300 bp

Location : /home/chumpol/AssemblyWS

• FASTA -> Reference sequence in FASTA formatted (cabV2.fa)

• FASTQ -> illumina paired-end reads in FASTQ formatted (cabV2_read1.fq.gz, cabV2_read2.fq.gz)

Preparing storage for raw reads

  • Login to server (158.108.144.7)
In [ ]:
ssh annotest@158.108.144.7
  • Create the directory for workshop
    • In [ ]:
    mkdir AssemblyWS
    In [31]:
    dirWS = "/home/annotest/AssemblyWS"
    In [32]:
    cd {dirWS}

    /home/annotest/AssemblyWS
    In [34]:
    %%bash
ln -s /home/chumpol/AssemblyWS/FASTQ .
    In [ ]:
    %%bash
ln -s /home/chumpol/AssemblyWS/FASTA .
  • Check raw data directory
    • In [39]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 30 Aug  7 15:52 FASTA -> /home/chumpol/AssemblyWS/FASTA/
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 30 Aug  7 15:52 FASTQ -> /home/chumpol/AssemblyWS/FASTQ/

    Velvet Assembler

    • Check the velvet executable files (velveth and velvetg)
    In [14]:
    %%bash
velveth

    velveth - simple hashing program
Version 1.2.10

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:
CATEGORIES = 6
MAXKMERLENGTH = 250
OPENMP
LONGSEQUENCES
BIGASSEMBLY

Usage:
./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]

	directory	: directory name for output files
	hash_length	: EITHER an odd integer (if even, it will be decremented) <= 250 (if above, will be reduced)
			: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 250 (if above, will be reduced)
				and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
	filename	: path to sequence file or - for standard input

File format options:
	-fasta	-fastq	-raw	-fasta.gz	-fastq.gz	-raw.gz	-sam	-bam	-fmtAuto
	(Note: -fmtAuto will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2

File layout options for paired reads (only for fasta and fastq formats):
	-interleaved	: File contains paired reads interleaved in the one file (default)
	-separate	: Read 2 separate files for paired reads

Read type options:
	-short	-shortPaired
	...
	-short5	-shortPaired5
	-short6	-shortPaired6
	-long	-longPaired
	-reference

Options:
	-strand_specific	: for strand specific transcriptome sequencing data (default: off)
	-reuse_Sequences	: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-reuse_binary	: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-noHash			: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
	-create_binary  	: create binary CnyUnifiedSeq file (default: off)

Synopsis:

- Short single end reads:
	velveth Assem 29 -short -fastq s_1_sequence.txt

- Paired-end short reads (remember to interleave paired reads):
	velveth Assem 31 -shortPaired -fasta interleaved.fna

- Paired-end short reads (using separate files for the paired reads)
	velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

- Two channels and some long reads:
	velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

- Three channels:
	velveth Assem 35 -shortPaired -fasta pe_lib1.fasta -shortPaired2 pe_lib2.fasta -short3 se_lib1.fa

Output:
	directory/Roadmaps
	directory/Sequences
		[Both files are picked up by graph, so please leave them there]
  • Create directory for running Velvet
    • In [41]:
    mkdir Velvet
  • Change directory to Velvet directory, create symbolic links of FASTQ files
    • In [47]:
    dirVelvet = "/home/annotest/AssemblyWS/Velvet"
    In [48]:
    cd {dirVelvet}

    /home/annotest/AssemblyWS/Velvet
    In [52]:
    %%bash
ln -s ../FASTQ/* .
    In [53]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:00 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:00 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Create shell script to run velvet (Run_Velvet.sh) with Nano / copy Run_Velvet.sh from /home/chumpol/AssemblyWS/Velvet/Run_Velvet.sh
    • In [54]:
    %%bash
cp /home/chumpol/AssemblyWS/Velvet/Run_Velvet.sh .
    In [55]:
    %%bash
more Run_Velvet.sh

    ::::::::::::::
Run_Velvet.sh
::::::::::::::
#!/bin/bash

# $1 as k-mer
# $2 input read

velveth Test_${1} $1 -fastq.gz -shortPaired -separate ${2}_read1.fq.gz ${2}_read2.fq.gz
velvetg Test_${1} -ins_length 300 -exp_cov 10 -cov_cutoff auto -min_contig_lgth 1000

    Parameters

    k-mers           : k-mers as first parameter ($1) of the script
-fastq.gz        : format of read files
-shortPaired -separate :  read type (Paired-end)
       Filename       : ${2} as second parameter of the script
-ins_length     : expected distance between two paired-end reads (300) 
-exp_cov        : expected coverage to infer (10)
      -cov_cutoff      : removal of low coverage nodes (auto)
      -min_contig_lgth : minimum contig length exported to contigs.fa file.
      Output is saved in Test_${1}
  • Run scripts
    • In [58]:
    %%bash
./Run_Velvet.sh 75 cabV2

    [0.000000] Reading FastQ file cabV2_read1.fq.gz;
[0.000291] Reading FastQ file cabV2_read2.fq.gz;
[5.013386] 925060 sequences found in total in the paired sequence files
[5.013390] Done
[5.026487] Reading read set file Test_75/Sequences;
[5.203390] 925060 sequences found
[5.976033] Done
[5.976037] 925060 sequences in total.
[5.976143] Writing into roadmap file Test_75/Roadmaps...
[6.359098] Inputting sequences...
[6.365410] Inputting sequence 0 / 925060
[8.983243]  === Sequences loaded in 2.624489 s
[8.985614] Done inputting sequences
[8.985616] Destroying splay table
[9.372377] Splay table destroyed
[0.000000] Reading roadmap file Test_75/Roadmaps
[1.225080] 925060 roadmaps read
[1.237108] Creating insertion markers
[1.393650] Ordering insertion markers
[1.419950] Counting preNodes
[1.559739] 1677039 preNodes counted, creating them now
[6.524007] Adjusting marker info...
[6.661250] Connecting preNodes
[7.019085] Cleaning up memory
[7.020495] Done creating preGraph
[7.020504] Concatenation...
[7.563851] Renumbering preNodes
[7.563894] Initial preNode count 1677039
[7.622448] Destroyed 1260839 preNodes
[7.622453] Concatenation over!
[7.622455] Clipping short tips off preGraph
[7.739048] Concatenation...
[7.911339] Renumbering preNodes
[7.911342] Initial preNode count 416200
[7.916685] Destroyed 392546 preNodes
[7.916687] Concatenation over!
[7.916687] 199487 tips cut off
[7.916688] 23654 nodes left
[7.916800] Writing into pregraph file Test_75/PreGraph...
[8.257118] Reading read set file Test_75/Sequences;
[8.435761] 925060 sequences found
[9.232938] Done
[9.638351] Reading pre-graph file Test_75/PreGraph
[9.638415] Graph has 23654 nodes and 925060 sequences
[9.802831] Scanning pre-graph file Test_75/PreGraph for k-mers
[9.957928] 5166917 kmers found
[10.568908] Sorting kmer occurence table ... 
[15.315342] Sorting done.
[15.315346] Computing acceleration table... 
[15.466536] Computing offsets... 
[15.604930] Ghost Threading through reads 0 / 925060
[16.031517]  === Ghost-Threaded in 0.441526 s
[16.031861] Threading through reads 0 / 925060
[17.042687]  === Threaded in 1.011161 s
[17.113997] Correcting graph with cutoff 0.200000
[17.117678] Determining eligible starting points
[17.146119] Done listing starting nodes
[17.146121] Initializing todo lists
[17.149003] Done with initilization
[17.149005] Activating arc lookup table
[17.152900] Done activating arc lookup table
[17.553726] 10000 / 23654 nodes visited
[17.930653] 20000 / 23654 nodes visited
[18.017725] Concatenation...
[18.018440] Renumbering nodes
[18.018441] Initial node count 23654
[18.018827] Removed 19478 null nodes
[18.018832] Concatenation over!
[18.018833] Clipping short tips off graph, drastic
[18.019700] Concatenation...
[18.043709] Renumbering nodes
[18.043710] Initial node count 4176
[18.043861] Removed 1023 null nodes
[18.043862] Concatenation over!
[18.043862] 3153 nodes left
[18.043953] Writing into graph file Test_75/Graph2...
[18.666390] Measuring median coverage depth...
[18.667539] Median coverage depth = 10.295438
[18.667582] Removing contigs with coverage < 5.147719...
[18.669440] Concatenation...
[18.714441] Renumbering nodes
[18.714442] Initial node count 3153
[18.714514] Removed 2090 null nodes
[18.714515] Concatenation over!
[18.714555] Concatenation...
[18.714631] Renumbering nodes
[18.714631] Initial node count 1063
[18.714633] Removed 0 null nodes
[18.714633] Concatenation over!
[18.714640] Clipping short tips off graph, drastic
[18.714741] Concatenation...
[18.715255] Renumbering nodes
[18.715256] Initial node count 1063
[18.715295] Removed 37 null nodes
[18.715296] Concatenation over!
[18.715296] 1026 nodes left
[18.715297] Read coherency...
[18.715305] Identifying unique nodes
[18.715334] Done, 791 unique nodes counted
[18.715335] Trimming read tips
[18.715424] Renumbering nodes
[18.715424] Initial node count 1026
[18.715426] Removed 0 null nodes
[18.715426] Confronted to 0 multiple hits and 0 null over 0
[18.715427] Read coherency over!
[18.722075] Starting pebble resolution...
[18.732289] Computing read to node mapping array sizes
[18.757604] Computing read to node mappings
[18.768573] Estimating library insert lengths...
[18.774250] Done
[18.774260] Computing direct node to node mappings
[18.788234] Scaffolding node 0
[18.798856]  === Nodes Scaffolded in 0.024595 s
[18.809034] Preparing to correct graph with cutoff 0.200000
[18.920196] Cleaning memory
[18.920267] Deactivating local correction settings
[18.920313] Pebble done.
[18.920314] Starting pebble resolution...
[18.929721] Computing read to node mapping array sizes
[18.949847] Computing read to node mappings
[18.962627] Estimating library insert lengths...
[18.972112] Done
[18.972119] Computing direct node to node mappings
[18.993819] Scaffolding node 0
[19.005947]  === Nodes Scaffolded in 0.033822 s
[19.014262] Preparing to correct graph with cutoff 0.200000
[19.020280] Cleaning memory
[19.020284] Deactivating local correction settings
[19.020312] Pebble done.
[19.020313] Concatenation...
[19.029035] Renumbering nodes
[19.029037] Initial node count 1026
[19.029114] Removed 631 null nodes
[19.029123] Concatenation over!
[19.029124] Removing reference contigs with coverage < 5.147719...
[19.029158] Concatenation...
[19.029170] Renumbering nodes
[19.029171] Initial node count 395
[19.029172] Removed 0 null nodes
[19.029178] Concatenation over!
[19.034808] Writing contigs into Test_75/contigs.fa...
[19.691495] Writing into stats file Test_75/stats.txt...
[19.696405] Writing into graph file Test_75/LastGraph...
[20.341936] Estimated Coverage cutoff = 5.147719
Final graph has 395 nodes and n50 of 55255, max 171853, total 4594714, using 860030/925060 reads

    The final contigs.fa is saved in Test_75 directory.

  • Try with another k-mers, such as 71, 81.

    • VelvetOptimiser

    Multi-threaded Perl script for automatically optimizing the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet assembler.

    • Create directory for running VelvetOptimiser
    In [59]:
    cd ..

    /home/annotest/AssemblyWS
    In [60]:
    pwd
    Out[60]:
    '/home/annotest/AssemblyWS'
    In [61]:
    mkdir VelvetOptimiser
  • Change directory to working directory, create symbolic links of FASTQ files.
    • In [62]:
    cd VelvetOptimiser

    /home/annotest/AssemblyWS/VelvetOptimiser
    In [63]:
    %%bash
ln -s ../FASTQ/* .
    In [64]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:06 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:06 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Create shell script to run VelvetOptimiser (Run_VelvetOptimiser.sh) with Nano / copy Run_VelvetOptimiser.sh from

    • /home/chumpol/AssemblyWS/VelvetOptimiser/Run_VelvetOptimiser.sh

    In [65]:
    cp /home/chumpol/AssemblyWS/VelvetOptimiser/Run_VelvetOptimiser.sh .
    In [66]:
    cat Run_VelvetOptimiser.sh

    #!/bin/env bash


# $1 is number of threads
# $2 is start k-mers
# $3 is stop k-mers
# $4 is read name

# Start from $1 to $2, step 5
/share/apps/VelvetOptimiser/VelvetOptimiser.pl -t $1 -s $2 -e $3 -x 5 -f "-shortPaired -separate -fastq.gz ${4}_read1.fq.gz ${4}_read2.fq.gz" -o "-ins_length 300 -exp_cov 10 -cov_cutoff auto -min_contig_lgth 1000"

    Parameters

     -t #        : number of CPU threads to use
 -s #        : start k-mers
 -e #        : stop k-mers
 -x #        : incremental steps of k-mers
 -f “string” : velveth parameters
 -o “string” : velvetg parameters
  • Run the scripts
    • In [67]:
    %%bash
./Run_VelvetOptimiser.sh 16 85 91 cabV2

    Logfile name: 07-08-2018-16-09-58_Logfile.txt

    ****************************************************
           VelvetOptimiser.pl Version 2.3.0-alpha
****************************************************
Number of CPUs available: 144
Current free RAM: 996.047GB
Velvet OMP compiler setting: 1
Aug  7 16:09:58 Starting to check input parameters.
	Old hash step value 5
	Hash search step value was odd, substracting one.  New hash step value = 4
	Velveth parameter string OK.
Aug  7 16:09:58 Finished checking input parameters.
Velvet details:
	Velvet version: 1.2.10
	Compiled categories: 6
	Compiled max kmer length: 250
	Maximum number of Velvet instances to run: 16
Will run velvet optimiser with the following paramters:
	Velveth parameter string:
		-shortPaired -separate -fastq.gz cabV2_read1.fq.gz cabV2_read2.fq.gz
	Velveth start hash values:	85
	Velveth end hash value:		91
	Velveth hash step value:	4
	Velvetg minimum coverage cutoff to use:	0

	Read tracking for final assembly off.
Aug  7 16:09:58 Beginning velveth runs.
Aug  7 16:09:58		Running velveth with hash value: 85.
Aug  7 16:10:00		Running velveth with hash value: 89.
Aug  7 16:10:03		Running velveth with hash value: 91.
Aug  7 16:10:09		Velveth with hash value 85 finished.
Aug  7 16:10:10		Velveth with hash value 89 finished.
Aug  7 16:10:13		Velveth with hash value 91 finished.
Aug  7 16:10:13 Finished velveth runs.
Aug  7 16:10:13 Beginning vanilla velvetg runs.
Aug  7 16:10:13		Running vanilla velvetg on hash value: 85
Aug  7 16:10:15		Running vanilla velvetg on hash value: 89
Aug  7 16:10:18		Running vanilla velvetg on hash value: 91
Aug  7 16:10:35		Velvetg on hash value: 85 finished.
Aug  7 16:10:36		Velvetg on hash value: 89 finished.
Aug  7 16:10:37		Velvetg on hash value: 91 finished.
Aug  7 16:10:37 Hash value of best assembly by assembly score: 91
Aug  7 16:10:37 Optimisation routine chosen for best assembly: shortPaired
Aug  7 16:10:37 Looking for the expected coverage
Aug  7 16:10:39		Expected coverage set to 7
Aug  7 16:10:39 Setting assembly short insert length(s) to auto
Aug  7 16:10:39 Beginning coverage cutoff optimisation
Aug  7 16:10:40		Setting cov_cutoff to 3.461.
Aug  7 16:10:44		Setting cov_cutoff to 2.139.
		Looking for best cutoff score between 0.000 and 5.600
		Max cutoff lies between 0.000 & 3.461
		fc = 4615188	fd = 4615398	abs diff = 210
Aug  7 16:10:47		Setting cov_cutoff to 1.322.
		Max cutoff lies between 0.000 & 2.139
		fc = 4615398	fd = 4615500	abs diff = 102
Aug  7 16:10:51		Setting cov_cutoff to 0.817.
		Max cutoff lies between 0.000 & 1.322
		fc = 4615500	fd = 4615500	abs diff = 0
Aug  7 16:10:54		Setting cov_cutoff to 0.505.
		Max cutoff lies between 0.505 & 1.322
		fc = 4615500	fd = 4615399	abs diff = 101
Aug  7 16:10:58		Setting cov_cutoff to 1.010.
		Optimum value of cutoff is 1.32
		Took 5 iterations
Aug  7 16:11:02


Final optimised assembly details:
********************************************************
Assembly id: 3
Assembly score: 4615405
Velveth timestamp: Aug  7 2018 16:10:13
Velvetg timestamp: Aug  7 2018 16:11:02
Velveth version: 1.2.10
Velvetg version: 1.2.10
Readfile(s): -shortPaired -separate -fastq.gz cabV2_read1.fq.gz cabV2_read2.fq.gz
Velveth parameter string: auto_data_91 91 -shortPaired -separate -fastq.gz cabV2_read1.fq.gz cabV2_read2.fq.gz
Velvetg parameter string: auto_data_91 -ins_length 300 -exp_cov 7 -cov_cutoff auto -min_contig_lgth 1000 -clean yes
Assembly directory: /home/annotest/AssemblyWS/VelvetOptimiser/auto_data_91
Velvet hash value: 91
Roadmap file size: 40716059
Total number of contigs: 345
n50: 22892
length of longest contig: 112538
Total bases in contigs: 4615405
Number of contigs > 1k: 345
Total bases in contigs > 1k: 4615405
Paired Library insert stats:
**********************************************************


Assembly output files are in the following directory:
/home/annotest/AssemblyWS/VelvetOptimiser/auto_data_91
    • Use 16 CPU cores
    • Vary k-mers from 75 - 91

    SPAdes assembler

    • Create directory for running SPAdes
    In [91]:
    cd ..

    /home/annotest/AssemblyWS
    In [71]:
    mkdir SPAdes
  • Change directory to working directory, create symbolic links of FASTQ files.
    • In [72]:
    cd SPAdes

    /home/annotest/AssemblyWS/SPAdes
    In [73]:
    %%bash
ln -s ../FASTQ/* .
    In [74]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:14 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:14 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Create shell script to run SPAdes (Run_SPAdes.sh) with Nano / copy Run_SPAdes.sh from

    • /home/chumpol/AssemblyWS/SPAdes/Run_SPAdes.sh

    In [75]:
    cp /home/chumpol/AssemblyWS/SPAdes/Run_SPAdes.sh .
    In [76]:
    cat Run_SPAdes.sh

    #!/bin/bash

# $1 as number of threads
# $2 as input file
# $3 as output directory

/share/apps/SPAdes-3.12.0-Linux/bin/spades.py -t $1 -1 ${2}_read1.fq.gz -2 ${2}_read2.fq.gz --only-assembler --cov-cutoff auto --careful -o $3

    Parameters

    -t #             : number of CPU threads to use
-1 file1         : paired read1 file
-2 file2         : paired read2 file
--only-assembler : runs only assembling (without read error correction)
--careful        : tries to reduce number of mismatches and short indels
-o output        : output directory
  • Run the script
    • In [77]:
    %%bash
./Run_SPAdes.sh 16 cabV2 SPAdes_Out

    Command line: /share/apps/SPAdes-3.12.0-Linux/bin/spades.py	-t	16	-1	/home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz	-2	/home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz	--only-assembler	--cov-cutoff	auto	--careful	-o	/home/annotest/AssemblyWS/SPAdes/SPAdes_Out	

System information:
  SPAdes version: 3.12.0
  Python version: 3.5.5
  OS: Linux-3.10.0-514.26.2.el7.x86_64-x86_64-with-centos-7.4.1708-Core

Output dir: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz']
      right reads: ['/home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned ON
  MismatchCorrector will be used
  Coverage cutoff is turned ON and threshold will be auto-detected
Other parameters:
  Dir for temp files: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp
  Threads: 16
  Memory limit (in Gb): 250


======= SPAdes pipeline started. Log can be found here: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/spades.log


===== Assembling started.


== Running assembler: K21

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K21/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K21/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=21
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  77)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  78)   Converting paired reads
  0:00:00.311    80M / 80M   INFO    General                 (binary_converter.hpp      :  93)   16384 reads processed
  0:00:00.557    96M / 96M   INFO    General                 (binary_converter.hpp      :  93)   32768 reads processed
  0:00:01.046   124M / 124M  INFO    General                 (binary_converter.hpp      :  93)   65536 reads processed
  0:00:02.009   180M / 180M  INFO    General                 (binary_converter.hpp      :  93)   131072 reads processed
  0:00:03.491   296M / 296M  INFO    General                 (binary_converter.hpp      :  93)   262144 reads processed
  0:00:07.294   468M / 468M  INFO    General                 (binary_converter.hpp      : 117)   462530 reads written
  0:00:07.844     4M / 468M  INFO    General                 (read_converter.hpp        :  87)   Converting single reads
  0:00:07.937   132M / 468M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:07.937     4M / 468M  INFO    General                 (read_converter.hpp        :  95)   Converting merged reads
  0:00:08.025   132M / 468M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:08.027     4M / 468M  INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:08.027     4M / 468M  INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:08.027     4M / 468M  INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:08.027     4M / 468M  INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:08.027     4M / 468M  INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:08.027     4M / 468M  INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:08.027     4M / 468M  INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 262144
  0:00:12.163     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:12.163     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:12.853    64M / 8G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:12.853    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:13.006    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 18798949 kmers in total.
  0:00:13.007    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:13.225    64M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:13.225    64M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:13.225    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:13.225    64M / 8G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:13.225    64M / 8G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:13.225    64M / 8G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 262144
  0:00:16.612     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 18798949 kmers
  0:00:16.612     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 18798949 kmers.
  0:00:17.289    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:17.435    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 18304331 kmers in total.
  0:00:17.435    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:17.613    64M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:18.206    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:18.388    64M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 8496152 bytes occupied (3.71329 bits per kmer).
  0:00:18.402    84M / 8G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:19.421    84M / 8G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:19.421    84M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Early tip clipping
  0:00:19.421    84M / 8G    INFO    General                 (construction.cpp          : 253)   Early tip clipper length bound set as (RL - K)
  0:00:19.421    84M / 8G    INFO   Early tip clipping       (early_simplification.hpp  : 181)   Early tip clipping
  0:00:21.321    84M / 8G    INFO   Early tip clipping       (early_simplification.hpp  : 184)   3269566 22-mers were removed by early tip clipper
  0:00:21.321    84M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:21.322    84M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:22.161   128M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 1390562 sequences extracted
  0:00:22.689   128M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:22.898   132M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:23.321   448M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:23.321   448M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:23.321   448M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:23.720   456M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 8725488 bytes occupied (3.71318 bits per kmer).
  0:00:23.747   528M / 8G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:25.616   528M / 8G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:26.337   528M / 8G    INFO    General                 (construction.cpp          : 464)   Processed 2781021 edges
  0:00:26.423   420M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 2
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 21
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 23. Coverage mad: 7.413
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:26.467   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:26.589   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:27.025   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:27.959   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 22.4523. Fitted coverage std. dev: 5.4301
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.872896
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 5
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 5
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4603800
  0:00:28.568   420M / 8G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 22.4523
  0:00:28.568   420M / 8G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 5
  0:00:28.569   420M / 8G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 1
  0:00:28.569   420M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:28.569   420M / 8G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:28.569   420M / 8G    INFO    General                 (graph_simplification.hpp  : 662)   Flanking coverage based disconnection disabled
  0:00:28.569   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:28.666   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 0 times
  0:00:28.666   420M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:28.666   420M / 8G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:28.666   420M / 8G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:28.667   420M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:28.667   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:28.831   404M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 466 times
  0:00:28.831   404M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:58.961   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 460110 times
  0:00:58.961   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:58.987   428M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:58.987   428M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:00:58.987   428M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 175 times
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:59.529   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 16646 times
  0:00:59.529   340M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:00:59.529   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.542   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 143 times
  0:00:59.542   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.172   316M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 3842 times
  0:01:00.172   316M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.208   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 1014 times
  0:01:00.208   308M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:01:00.208   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.212   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.212   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.288   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 129 times
  0:01:00.288   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.303   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 516 times
  0:01:00.303   304M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:01:00.303   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.304   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 1 times
  0:01:00.304   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.335   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 80 times
  0:01:00.335   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 62 times
  0:01:00.338   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.345   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 15 times
  0:01:00.345   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 54 times
  0:01:00.346   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.350   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 8 times
  0:01:00.350   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 18 times
  0:01:00.352   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 3 times
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 26 times
  0:01:00.353   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 2 times
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 11 times
  0:01:00.354   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.355   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 19 times
  0:01:00.355   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:01:00.355   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.359   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.359   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.459   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 110 times
  0:01:00.459   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:00.464   296M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:00.464   296M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:01:00.464   296M / 8G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:01:00.464   296M / 8G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:01:00.464   296M / 8G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:01:00.464   296M / 8G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.468   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.468   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.547   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 9 times
  0:01:00.547   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.550   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.550   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:00.624   296M / 8G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:01:00.646   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:01:00.648   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 0 times
  0:01:00.648   296M / 8G    INFO    General                 (simplification.cpp        : 340)   Removing all the edges having coverage 1 and less
  0:01:00.651   296M / 8G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:00.659   296M / 8G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 25.6143
  0:01:00.659   296M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:00.659   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph_with_scaffolds.gfa
  0:01:00.772   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/before_rr.fasta
  0:01:00.902   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph.fastg
  0:01:01.376   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/simplified_contigs.fasta
  0:01:01.511   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/final_contigs.fasta
  0:01:01.645   296M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:01.645   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph_with_scaffolds.gfa
  0:01:01.762   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/before_rr.fasta
  0:01:01.893   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph.fastg
  0:01:02.369   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/simplified_contigs.fasta
  0:01:02.508   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/final_contigs.fasta
  0:01:02.655   296M / 8G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:01:02.951    64M / 8G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 1 minutes 2 seconds
Max read length detected as 151
Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150

== Running assembler: K33

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K33/configs/config.info
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K33/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=33
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  59)   Binary reads detected
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:00.002     4M / 4M    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.002     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:00.002     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:04.181     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:04.181     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:06.101    64M / 9G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:06.101    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:06.407    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 23619460 kmers in total.
  0:00:06.408    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:06.840    64M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:06.840    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:06.840    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:06.840    64M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:06.840    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:06.840    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:10.574     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 23619460 kmers
  0:00:10.574     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 23619460 kmers.
  0:00:11.367    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:11.580    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 23286214 kmers in total.
  0:00:11.580    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:12.048    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:12.916    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:13.381    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 10806120 bytes occupied (3.71245 bits per kmer).
  0:00:13.397    88M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:14.675    88M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:14.675    88M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Early tip clipping
  0:00:14.676    88M / 9G    INFO    General                 (construction.cpp          : 253)   Early tip clipper length bound set as (RL - K)
  0:00:14.676    88M / 9G    INFO   Early tip clipping       (early_simplification.hpp  : 181)   Early tip clipping
  0:00:16.978    88M / 9G    INFO   Early tip clipping       (early_simplification.hpp  : 184)   7137863 34-mers were removed by early tip clipper
  0:00:16.979    88M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:16.980    88M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:18.027   124M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 962429 sequences extracted
  0:00:18.593   124M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:18.893   124M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:19.292   348M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:19.293   348M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:19.293   348M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:19.799   372M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 10960640 bytes occupied (3.71241 bits per kmer).
  0:00:19.842   464M / 9G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:21.816   464M / 9G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:22.648   464M / 9G    INFO    General                 (construction.cpp          : 464)   Processed 1924843 edges
  0:00:22.774   312M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 0
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 18
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 19. Coverage mad: 7.413
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:22.799   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:22.869   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:23.131   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:23.776   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:24.508   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 18.8784. Fitted coverage std. dev: 5.07148
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.999913
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 4
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 4
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4707199
  0:00:24.509   308M / 9G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 18.8784
  0:00:24.509   308M / 9G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 4
  0:00:24.509   308M / 9G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 0
  0:00:24.509   308M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:24.509   308M / 9G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:24.509   308M / 9G    INFO    General                 (graph_simplification.hpp  : 662)   Flanking coverage based disconnection disabled
  0:00:24.509   308M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:24.586   308M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 0 times
  0:00:24.586   308M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:24.586   308M / 9G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:24.586   308M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:24.586   308M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:24.586   308M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:24.729   296M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 915 times
  0:00:24.729   296M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:45.998   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 322286 times
  0:00:45.998   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.005   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 5 times
  0:00:46.005   268M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:00:46.005   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.038   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 352 times
  0:00:46.038   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 3 times
  0:00:46.039   244M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.173   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 4132 times
  0:00:46.173   224M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:00:46.173   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.175   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 86 times
  0:00:46.175   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.257   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 701 times
  0:00:46.257   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 64 times
  0:00:46.258   216M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.260   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 7 times
  0:00:46.260   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 68 times
  0:00:46.262   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 22 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 8 times
  0:00:46.266   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 3 times
  0:00:46.266   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 9 times
  0:00:46.267   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 5 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:46.267   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.268   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 9 times
  0:00:46.268   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:00:46.268   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.270   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.270   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.313   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 25 times
  0:00:46.313   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:46.318   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.319   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:46.319   212M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:00:46.319   212M / 9G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:00:46.319   212M / 9G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:00:46.319   212M / 9G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:00:46.319   212M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:46.319   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.321   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.321   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.353   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:46.353   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.355   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.355   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.386   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.386   204M / 9G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:00:46.396   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:00:46.398   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 11 times
  0:00:46.398   204M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:46.402   204M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 21.7425
  0:00:46.402   204M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:00:46.402   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph_with_scaffolds.gfa
  0:00:46.483   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/before_rr.fasta
  0:00:46.579   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph.fastg
  0:00:46.910   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/simplified_contigs.fasta
  0:00:47.002   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/final_contigs.fasta
  0:00:47.097   204M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:00:47.097   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph_with_scaffolds.gfa
  0:00:47.175   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/before_rr.fasta
  0:00:47.272   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph.fastg
  0:00:47.608   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/simplified_contigs.fasta
  0:00:47.704   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/final_contigs.fasta
  0:00:47.807   204M / 9G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:00:47.955    68M / 9G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 0 minutes 47 seconds

== Running assembler: K55

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K55/configs/config.info
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K55/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=55
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  76)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  59)   Binary reads detected
  0:00:00.001     4M / 4M    INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:00.001     4M / 4M    INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:00.001     4M / 4M    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.002     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:00.002     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:04.658     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:04.658     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:06.935    64M / 9G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:06.935    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:07.293    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28314268 kmers in total.
  0:00:07.293    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:07.877    64M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:07.877    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:07.877    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:07.877    64M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:07.877    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:07.877    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:12.066     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 28314268 kmers
  0:00:12.066     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 28314268 kmers.
  0:00:12.876    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:13.131    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28202227 kmers in total.
  0:00:13.131    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:13.652    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:14.854    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:15.411    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13085528 bytes occupied (3.71191 bits per kmer).
  0:00:15.432    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:16.895    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:16.896    92M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:16.897    92M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:18.486   188M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 1389218 sequences extracted
  0:00:19.394   188M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:19.745   188M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:20.336   516M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:20.336   516M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:20.336   516M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:20.903   524M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13137352 bytes occupied (3.71187 bits per kmer).
  0:00:20.970   636M / 9G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:22.758   636M / 9G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:24.249   636M / 9G    INFO    General                 (construction.cpp          : 464)   Processed 2778430 edges
  0:00:24.444   472M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 0
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 13
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 13. Coverage mad: 5.9304
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:24.456   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:24.487   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:24.595   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:24.841   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:25.460   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 32
  0:00:26.235   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 64
  0:00:26.428   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 13.4147. Fitted coverage std. dev: 4.27326
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.999714
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 4
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 4
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4788539
  0:00:26.429   468M / 9G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 13.4147
  0:00:26.429   468M / 9G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 4
  0:00:26.429   468M / 9G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 0
  0:00:26.429   468M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:00:26.429   468M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:00:26.429   468M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:26.429   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:26.429   468M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:26.429   468M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.19881 Gb
  0:00:26.429   468M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:29.421     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 2778430 edges
  0:00:29.421     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 2778430 sequences.
  0:00:30.192   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:30.427   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28314268 kmers in total.
  0:00:30.427   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:30.885   468M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:32.287   488M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:32.894   488M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13137352 bytes occupied (3.71187 bits per kmer).
  0:00:33.194     1G / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:00:34.116     1G / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:00:34.116     1G / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:00:36.204     1G / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:00:36.827     1G / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:00:36.827     1G / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:00:37.296     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:00:40.791     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 42 gaps after checking 620 candidates
  0:00:40.897     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:40.902   480M / 9G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:40.902   480M / 9G    INFO    General                 (graph_simplification.hpp  : 662)   Flanking coverage based disconnection disabled
  0:00:40.902   480M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:41.018   480M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 1 times
  0:00:41.018   480M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:41.018   480M / 9G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:41.019   480M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:41.019   480M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:41.019   480M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:47.765   492M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 538227 times
  0:00:47.765   492M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.261   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 113653 times
  0:01:18.262   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.267  1000M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 2 times
  0:01:18.267  1000M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:01:18.267  1000M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.285   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 558 times
  0:01:18.285   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 6 times
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 4 times
  0:01:18.287   992M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.311   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 789 times
  0:01:18.311   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:01:18.311   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.313   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 102 times
  0:01:18.313   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 108 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 5 times
  0:01:18.342   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 7 times
  0:01:18.342   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 1 times
  0:01:18.343   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 8 times
  0:01:18.343   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 18 times
  0:01:18.344   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 38 times
  0:01:18.346   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.351   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 76 times
  0:01:18.351   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:01:18.351   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.354   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.354   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.382   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 6 times
  0:01:18.382   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:18.386   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:18.386   988M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:01:18.386   988M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:01:18.386   988M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:01:18.386   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:01:18.386   988M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:01:18.386   988M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.18823 Gb
  0:01:18.386   988M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:01:20.765     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 38109 edges
  0:01:20.765     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 38109 sequences.
  0:01:21.696   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:01:21.819   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 5432667 kmers in total.
  0:01:21.819   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:01:21.947   988M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:01:22.072  1000M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:01:22.177  1000M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 2527456 bytes occupied (3.72186 bits per kmer).
  0:01:22.316     1G / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:01:22.439     1G / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:01:22.439     1G / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:01:22.466     1G / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:01:24.538     1G / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:01:24.538     1G / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:01:24.543     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:01:24.588     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 0 gaps after checking 24 candidates
  0:01:24.591     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:01:24.591     1G / 9G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:01:24.591     1G / 9G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:01:24.591     1G / 9G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:01:24.591     1G / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:01:24.591     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:24.595     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:24.595     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:24.615     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:24.615     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:24.618     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:24.618     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:24.636     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:24.636     1G / 9G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:01:24.651     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:01:25.067     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 6674 times
  0:01:25.067     1G / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:25.078     1G / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 14.9594
  0:01:25.078     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:25.078     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph_with_scaffolds.gfa
  0:01:25.153     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/before_rr.fasta
  0:01:25.235     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph.fastg
  0:01:25.528     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/simplified_contigs.fasta
  0:01:25.610     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/final_contigs.fasta
  0:01:25.690     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:25.690     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph_with_scaffolds.gfa
  0:01:25.766     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/before_rr.fasta
  0:01:25.848     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph.fastg
  0:01:26.140     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/simplified_contigs.fasta
  0:01:26.225     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/final_contigs.fasta
  0:01:26.312     1G / 9G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:01:31.344    72M / 9G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 1 minutes 31 seconds

== Running assembler: K77

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K77/configs/config.info
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K77/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=77
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  76)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.002     4M / 4M    INFO    General                 (read_converter.hpp        :  59)   Binary reads detected
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:00.002     4M / 4M    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.002     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:00.002     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:05.302     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:05.302     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:07.111    64M / 9G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:07.111    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:08.494    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28724894 kmers in total.
  0:00:08.494    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:09.412    64M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:09.412    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:09.412    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:09.412    64M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:09.412    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:09.412    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:14.039     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 28724894 kmers
  0:00:14.039     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 28724894 kmers.
  0:00:14.810    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:15.275    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28787624 kmers in total.
  0:00:15.275    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:16.031    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:17.075    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:18.029    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13356976 bytes occupied (3.71187 bits per kmer).
  0:00:18.052    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:19.604    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:19.605    92M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:19.607    92M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:21.398   192M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 1160163 sequences extracted
  0:00:22.400   192M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:22.759   192M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:23.348   464M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:23.348   464M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:23.348   464M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:24.158   468M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13327808 bytes occupied (3.71185 bits per kmer).
  0:00:24.220   580M / 9G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:25.615   580M / 9G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:27.014   580M / 9G    INFO    General                 (construction.cpp          : 464)   Processed 2320325 edges
  0:00:27.222   428M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 2
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 8
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 9. Coverage mad: 4.4478
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:27.231   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:27.252   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:27.323   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:27.472   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:27.697   424M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 32
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 9.19109. Fitted coverage std. dev: 3.34463
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.354172
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 5
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 5
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4449079
  0:00:27.802   420M / 9G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 9.19109
  0:00:27.802   420M / 9G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 5
  0:00:27.802   420M / 9G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 1
  0:00:27.802   420M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:00:27.802   420M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:00:27.802   420M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:27.802   420M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:27.802   420M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:27.802   420M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.19979 Gb
  0:00:27.802   420M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:31.220     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 2320325 edges
  0:00:31.220     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 2320325 sequences.
  0:00:31.904   416M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:32.333   416M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28724894 kmers in total.
  0:00:32.333   416M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:33.009   416M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:34.197   440M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:35.166   440M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13327808 bytes occupied (3.71185 bits per kmer).
  0:00:35.435     1G / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:00:36.291     1G / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:00:36.292     1G / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:00:38.167     1G / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:00:38.744     1G / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:00:38.744     1G / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:00:39.262     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:00:42.495     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 82 gaps after checking 1106 candidates
  0:00:42.691     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:42.697   432M / 9G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:42.697   432M / 9G    INFO    General                 (simplification.cpp        :  62)   Most init cleaning disabled on main iteration
  0:00:42.697   432M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:42.797   432M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 0 times
  0:00:42.797   432M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:42.797   432M / 9G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:42.797   432M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:42.797   432M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:42.797   432M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:51.729   380M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 551441 times
  0:00:51.729   380M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.255   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1919 times
  0:00:52.255   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.276   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:52.276   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:00:52.276   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 12 times
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.280   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 94 times
  0:00:52.280   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:00:52.280   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.282   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 60 times
  0:00:52.282   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 9 times
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 3 times
  0:00:52.286   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 18 times
  0:00:52.287   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.288   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:52.288   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.291   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 85 times
  0:00:52.291   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:00:52.291   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.291   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.292   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.292   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.292   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 257 times
  0:00:52.305   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 443 times
  0:00:52.329   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 607 times
  0:00:52.363   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 572 times
  0:00:52.398   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.438   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 503 times
  0:00:52.438   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:00:52.438   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.455   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 1 times
  0:00:52.455   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.481   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.481   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:52.496   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:52.496   392M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:00:52.496   392M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:00:52.497   392M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:52.497   392M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:52.497   392M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:52.497   392M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20036 Gb
  0:00:52.497   392M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:55.146     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 142399 edges
  0:00:55.146     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 142399 sequences.
  0:00:55.840   388M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:56.003   388M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 9706450 kmers in total.
  0:00:56.003   388M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:56.238   388M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:56.487   392M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:56.792   392M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 4508952 bytes occupied (3.71625 bits per kmer).
  0:00:57.029   616M / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:00:57.304   616M / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:00:57.305   616M / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:00:57.515   636M / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:00:58.964   636M / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:00:58.964   636M / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:00:59.042   616M / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:00:59.203   616M / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 1 gaps after checking 181 candidates
  0:00:59.242   616M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:00:59.242   616M / 9G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:00:59.242   616M / 9G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:00:59.242   616M / 9G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:00:59.242   616M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:59.242   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.273   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:59.273   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:59.297   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:59.297   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.314   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:59.314   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:59.335   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:59.335   616M / 9G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:00:59.432   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:01:03.531   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 68071 times
  0:01:03.531   392M / 9G    INFO    General                 (simplification.cpp        : 340)   Removing all the edges having coverage 1 and less
  0:01:03.532   392M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:03.533   392M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 9.393
  0:01:03.533   392M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Mismatch Correction
  0:01:03.533   392M / 9G    INFO    General                 (graph_pack.hpp            : 109)   Normalizing k-mer map. Total 311881 kmers to process
  0:01:03.724   388M / 9G    INFO    General                 (graph_pack.hpp            : 111)   Normalizing done
  0:01:06.678   400M / 9G    INFO    General                 (mismatch_shall_not_pass.hp: 189)   Finished collecting potential mismatches positions
  0:01:06.774   388M / 9G    INFO    General                 (mismatch_shall_not_pass.hp: 290)   All edges processed
  0:01:06.775   388M / 9G    INFO    General                 (mismatch_correction.cpp   :  27)   Corrected 0 nucleotides
  0:01:06.776   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:06.776   388M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph_with_scaffolds.gfa
  0:01:06.838   388M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/before_rr.fasta
  0:01:06.900   388M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph.fastg
  0:01:07.127   388M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/simplified_contigs.fasta
  0:01:07.203   388M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/intermediate_contigs.fasta
  0:01:07.279   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Paired Information Counting
  0:01:07.292   388M / 9G    INFO    General                 (graph_pack.hpp            : 109)   Normalizing k-mer map. Total 311881 kmers to process
  0:01:07.292   388M / 9G    INFO    General                 (graph_pack.hpp            : 111)   Normalizing done
  0:01:07.293   388M / 9G    INFO    General                 (pair_info_count.cpp       : 320)   Min edge length for estimation: 6989
  0:01:07.293   388M / 9G    INFO    General                 (pair_info_count.cpp       : 331)   Estimating insert size for library #0
  0:01:07.293   388M / 9G    INFO    General                 (pair_info_count.cpp       : 190)   Estimating insert size (takes a while)
  0:01:07.397   660M / 9G    INFO    General                 (pair_info_count.cpp       :  39)   Selecting usual mapper
  0:01:09.274   660M / 9G    INFO    General                 (sequence_mapper_notifier.h:  98)   Total 462530 reads processed
  0:01:10.663   660M / 9G    INFO    General                 (pair_info_count.cpp       : 209)   Edge pairs: 67108864 (rough upper limit)
  0:01:10.663   660M / 9G    INFO    General                 (pair_info_count.cpp       : 213)   189193 paired reads (40.9039% of all) aligned to long edges
  0:01:10.665   388M / 9G    INFO    General                 (pair_info_count.cpp       : 354)     Insert size = 300.004, deviation = 29.9794, left quantile = 262, right quantile = 338, read length = 151
  0:01:10.730   580M / 9G    INFO    General                 (pair_info_count.cpp       : 371)   Filtering data for library #0
  0:01:10.730   580M / 9G    INFO    General                 (pair_info_count.cpp       :  39)   Selecting usual mapper
  0:01:12.298   580M / 9G    INFO    General                 (sequence_mapper_notifier.h:  98)   Total 462530 reads processed
  0:01:12.298   580M / 9G    INFO    General                 (pair_info_count.cpp       : 383)   Mapping library #0
  0:01:12.298   580M / 9G    INFO    General                 (pair_info_count.cpp       : 385)   Mapping paired reads (takes a while)
  0:01:12.298   580M / 9G    INFO    General                 (pair_info_count.cpp       : 289)   Left insert size quantile 262, right insert size quantile 338, filtering threshold 2, rounding threshold 0
  0:01:12.310   592M / 9G    INFO    General                 (pair_info_count.cpp       :  39)   Selecting usual mapper
  0:01:13.865   592M / 9G    INFO    General                 (sequence_mapper_notifier.h:  98)   Total 462530 reads processed
  0:01:13.877   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Distance Estimation
  0:01:13.877   388M / 9G    INFO    General                 (distance_estimation.cpp   : 173)   Processing library #0
  0:01:13.877   388M / 9G    INFO    General                 (distance_estimation.cpp   : 149)   Weight Filter Done
  0:01:13.877   388M / 9G    INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:01:13.910   388M / 9G    INFO    General                 (distance_estimation.cpp   :  34)   Filtering info
  0:01:13.910   388M / 9G    INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; index size: 17495
  0:01:13.921   392M / 9G    INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering
  0:01:13.921   388M / 9G    INFO    General                 (distance_estimation.cpp   : 156)   Refining clustered pair information
  0:01:13.927   388M / 9G    INFO    General                 (distance_estimation.cpp   : 158)   The refining of clustered pair information has been finished
  0:01:13.927   388M / 9G    INFO    General                 (distance_estimation.cpp   : 160)   Improving paired information
  0:01:13.947   388M / 9G    INFO   PairInfoImprover         (pair_info_improver.hpp    : 103)   Paired info stats: missing = 620; contradictional = 628
  0:01:13.967   388M / 9G    INFO   PairInfoImprover         (pair_info_improver.hpp    : 103)   Paired info stats: missing = 33; contradictional = 0
  0:01:13.967   388M / 9G    INFO    General                 (distance_estimation.cpp   : 103)   Filling scaffolding index
  0:01:13.967   388M / 9G    INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SMOOTHING distance estimator
  0:01:13.971   388M / 9G    INFO    General                 (distance_estimation.cpp   :  34)   Filtering info
  0:01:13.971   388M / 9G    INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; index size: 6265
  0:01:13.974   388M / 9G    INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering
  0:01:13.974   388M / 9G    INFO    General                 (distance_estimation.cpp   : 182)   Clearing raw paired index
  0:01:13.977   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Repeat Resolving
  0:01:13.977   388M / 9G    INFO    General                 (repeat_resolving.cpp      :  69)   Using Path-Extend repeat resolving
  0:01:13.977   388M / 9G    INFO    General                 (launcher.cpp              : 477)   ExSPAnder repeat resolving tool started
  0:01:13.992   400M / 9G    INFO    General                 (launcher.cpp              : 392)   Creating main extenders, unique edge length = 2000
  0:01:13.992   400M / 9G    INFO    General                 (extenders_logic.cpp       : 275)   Estimated coverage of library #0 is 9.393
  0:01:13.993   400M / 9G    INFO    General                 (extenders_logic.cpp       : 275)   Estimated coverage of library #0 is 9.393
  0:01:13.994   400M / 9G    INFO    General                 (extenders_logic.cpp       : 472)   Using 1 paired-end library
  0:01:13.994   400M / 9G    INFO    General                 (extenders_logic.cpp       : 473)   Using 1 paired-end scaffolding library
  0:01:13.994   400M / 9G    INFO    General                 (extenders_logic.cpp       : 474)   Using 0 single read libraries
  0:01:13.994   400M / 9G    INFO    General                 (launcher.cpp              : 420)   Total number of extenders is 3
  0:01:13.994   400M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 0 paths from 3082 (0%)
  0:01:14.011   400M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 128 paths from 3082 (4%)
  0:01:14.022   404M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 256 paths from 3082 (8%)
  0:01:14.027   404M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 309 paths from 3082 (10%)
  0:01:14.052   404M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 512 paths from 3082 (16%)
  0:01:14.066   404M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 618 paths from 3082 (20%)
  0:01:14.107   408M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 927 paths from 3082 (30%)
  0:01:14.114   408M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 1024 paths from 3082 (33%)
  0:01:14.153   412M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 1236 paths from 3082 (40%)
  0:01:14.229   416M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 1545 paths from 3082 (50%)
  0:01:14.299   416M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 1854 paths from 3082 (60%)
  0:01:14.343   420M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 2048 paths from 3082 (66%)
  0:01:14.365   420M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 2163 paths from 3082 (70%)
  0:01:14.432   424M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 2472 paths from 3082 (80%)
  0:01:14.508   428M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 2781 paths from 3082 (90%)
  0:01:14.532   428M / 9G    INFO    General                 (launcher.cpp              : 234)   Finalizing paths
  0:01:14.532   428M / 9G    INFO    General                 (launcher.cpp              : 236)   Deduplicating paths
  0:01:14.546   420M / 9G    INFO    General                 (launcher.cpp              : 240)   Paths deduplicated
  0:01:14.546   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 295)   Removing overlaps
  0:01:14.546   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 298)   Sorting paths
  0:01:14.546   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 305)   Marking overlaps
  0:01:14.546   420M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 130)   Marking start/end overlaps
  0:01:14.549   420M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 133)   Marking remaining overlaps
  0:01:14.551   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 308)   Splitting paths
  0:01:14.554   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 313)   Deduplicating paths
  0:01:14.557   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 315)   Overlaps removed
  0:01:14.561   420M / 9G    INFO    General                 (launcher.cpp              : 257)   Paths finalized
  0:01:14.561   420M / 9G    INFO    General                 (launcher.cpp              : 427)   Closing gaps in paths
  0:01:14.568   424M / 9G    INFO    General                 (launcher.cpp              : 455)   Gap closing completed
  0:01:14.570   424M / 9G    INFO    General                 (launcher.cpp              : 286)   Traversing tandem repeats
  0:01:14.594   424M / 9G    INFO    General                 (launcher.cpp              : 296)   Traversed 549 loops
  0:01:14.594   424M / 9G    INFO    General                 (launcher.cpp              : 234)   Finalizing paths
  0:01:14.594   424M / 9G    INFO    General                 (launcher.cpp              : 236)   Deduplicating paths
  0:01:14.595   424M / 9G    INFO    General                 (launcher.cpp              : 240)   Paths deduplicated
  0:01:14.595   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 295)   Removing overlaps
  0:01:14.595   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 298)   Sorting paths
  0:01:14.596   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 305)   Marking overlaps
  0:01:14.596   424M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 130)   Marking start/end overlaps
  0:01:14.597   424M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 133)   Marking remaining overlaps
  0:01:14.598   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 308)   Splitting paths
  0:01:14.599   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 313)   Deduplicating paths
  0:01:14.599   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 315)   Overlaps removed
  0:01:14.601   424M / 9G    INFO    General                 (launcher.cpp              : 257)   Paths finalized
  0:01:14.604   424M / 9G    INFO    General                 (launcher.cpp              : 529)   ExSPAnder repeat resolving tool finished
  0:01:14.625   400M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:14.625   400M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph_with_scaffolds.gfa
  0:01:14.676   400M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/before_rr.fasta
  0:01:14.739   400M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph.fastg
  0:01:14.954   404M / 9G    INFO    General                 (contig_output_stage.cpp   :  20)   Outputting FastG paths to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/final_contigs.paths
  0:01:15.046   400M / 9G    INFO    General                 (contig_output_stage.cpp   :  20)   Outputting FastG paths to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/scaffolds.paths
  0:01:15.116   400M / 9G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:01:15.296    68M / 9G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 1 minutes 15 seconds

===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77 


===== Mismatch correction started.

== Processing of scaffolds


== Running contig polishing tool: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-corrector-core /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/scaffolds/configs/corrector.info /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta


== Dataset description file was created: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/scaffolds/configs/corrector.info

/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/scaffolds/configs/log.properties  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  58)   Starting MismatchCorrector, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  59)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 195)   Splitting assembly...
  0:00:00.000     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 196)   Assembly file: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta
  0:00:00.174     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 203)   Processing paired sublib of number 0
  0:00:00.174     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 206)   /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
  0:00:00.174     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 140)   Running bwa index ...: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta
[bwa_index] Pack FASTA... 0.07 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.31 seconds elapse.
[bwa_index] Update BWT... 0.06 sec
[bwa_index] Pack forward-only FASTA... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 0.75 sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta
[main] Real time: 2.265 sec; CPU: 2.259 sec
  0:00:02.442     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 149)   Running bwa mem ...:/home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem  -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz  > /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_o5hhdch0/lib0_VA0t3N/tmp.sam
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
[main] Real time: 9.495 sec; CPU: 87.977 sec
  0:00:11.999     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 209)   Adding samfile /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_o5hhdch0/lib0_VA0t3N/tmp.sam
  0:00:15.975    60M / 60M   INFO   DatasetProcessor         (dataset_processor.cpp     : 105)   processed 1000000reads, flushing
  0:00:16.183    20M / 60M   INFO   DatasetProcessor         (dataset_processor.cpp     : 235)   Processing contigs
  0:00:17.116   260M / 264M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_16_length_68666_cov_9.322297 processed with 27 changes in thread 11
  0:00:17.186   280M / 284M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_15_length_75367_cov_9.330734 processed with 31 changes in thread 14
  0:00:17.203   284M / 284M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_14_length_79082_cov_9.256731 processed with 30 changes in thread 10
  0:00:17.266   288M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_12_length_80943_cov_9.156667 processed with 47 changes in thread 5
  0:00:17.277   284M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_13_length_79621_cov_9.427487 processed with 22 changes in thread 3
  0:00:17.321   280M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_11_length_86382_cov_9.255362 processed with 41 changes in thread 13
  0:00:17.327   268M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_10_length_91841_cov_9.187971 processed with 40 changes in thread 0
  0:00:17.444   276M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_9_length_93568_cov_9.157053 processed with 61 changes in thread 4
  0:00:17.531   272M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_8_length_102123_cov_9.304206 processed with 45 changes in thread 15
  0:00:17.564   264M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_5_length_105317_cov_9.323489 processed with 53 changes in thread 1
  0:00:17.568   260M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_6_length_103454_cov_9.340192 processed with 46 changes in thread 7
  0:00:17.638   248M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_7_length_103373_cov_9.283738 processed with 42 changes in thread 2
  0:00:17.713   240M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_4_length_117049_cov_9.316383 processed with 56 changes in thread 9
  0:00:17.840   232M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_3_length_127286_cov_9.299499 processed with 56 changes in thread 8
  0:00:17.860   220M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_17_length_67221_cov_9.148710 processed with 42 changes in thread 11
  0:00:17.918   216M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_19_length_59516_cov_9.118121 processed with 41 changes in thread 10
  0:00:17.949   212M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_21_length_58500_cov_9.342707 processed with 40 changes in thread 3
  0:00:17.953   208M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_20_length_59353_cov_9.146029 processed with 45 changes in thread 5
  0:00:17.965   204M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_2_length_140662_cov_9.276381 processed with 60 changes in thread 12
  0:00:17.965   204M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_22_length_56255_cov_9.120474 processed with 32 changes in thread 13
  0:00:17.974   188M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_1_length_142002_cov_9.288807 processed with 83 changes in thread 6
  0:00:17.976   188M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_23_length_54525_cov_9.206270 processed with 20 changes in thread 0
  0:00:18.097   168M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_18_length_61016_cov_9.145982 processed with 36 changes in thread 14
  0:00:18.153   164M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_25_length_53628_cov_9.122052 processed with 46 changes in thread 15
  0:00:18.172   160M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_26_length_52671_cov_8.958684 processed with 29 changes in thread 1
  0:00:18.195   156M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_24_length_54285_cov_9.341924 processed with 32 changes in thread 4
  0:00:18.231   152M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_28_length_49923_cov_9.205292 processed with 32 changes in thread 2
  0:00:18.272   152M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_27_length_51962_cov_9.223783 processed with 15 changes in thread 7
  0:00:18.303   148M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_29_length_49269_cov_9.104692 processed with 32 changes in thread 9
  0:00:18.412   144M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_32_length_44267_cov_9.305386 processed with 17 changes in thread 10
  0:00:18.426   144M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_30_length_46027_cov_9.221349 processed with 19 changes in thread 8
  0:00:18.444   140M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_34_length_42977_cov_9.193357 processed with 25 changes in thread 5
  0:00:18.450   140M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_31_length_45461_cov_9.278821 processed with 20 changes in thread 11
  0:00:18.452   136M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_38_length_40177_cov_9.005012 processed with 20 changes in thread 6
  0:00:18.452   132M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_37_length_40871_cov_9.215571 processed with 14 changes in thread 0
  0:00:18.459   128M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_33_length_42997_cov_9.426375 processed with 14 changes in thread 3
  0:00:18.461   128M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_36_length_42333_cov_9.380561 processed with 13 changes in thread 12
  0:00:18.462   120M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_35_length_42826_cov_9.105312 processed with 29 changes in thread 13
  0:00:18.578   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_39_length_39763_cov_9.213929 processed with 21 changes in thread 14
  0:00:18.611   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_42_length_36235_cov_9.288484 processed with 27 changes in thread 4
  0:00:18.619   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_40_length_39706_cov_9.178480 processed with 28 changes in thread 15
  0:00:18.631   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_41_length_39340_cov_9.266689 processed with 10 changes in thread 1
  0:00:18.683   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_44_length_35354_cov_9.258951 processed with 15 changes in thread 7
  0:00:18.687   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_43_length_35960_cov_9.286542 processed with 11 changes in thread 2
  0:00:18.717   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_45_length_35098_cov_9.382456 processed with 7 changes in thread 9
  0:00:18.762   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_54_length_27094_cov_9.077100 processed with 9 changes in thread 13
  0:00:18.791   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_53_length_28791_cov_9.096399 processed with 12 changes in thread 12
  0:00:18.797   104M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_52_length_29416_cov_8.992501 processed with 26 changes in thread 3
  0:00:18.802   100M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_46_length_34659_cov_9.288271 processed with 17 changes in thread 10
  0:00:18.821    96M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_50_length_31620_cov_9.175221 processed with 20 changes in thread 0
  0:00:18.824    96M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_48_length_32089_cov_9.280301 processed with 21 changes in thread 5
  0:00:18.869    92M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_55_length_26224_cov_9.265537 processed with 12 changes in thread 14
  0:00:18.879    92M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_47_length_32658_cov_9.352353 processed with 15 changes in thread 8
  0:00:18.887    88M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_49_length_31943_cov_9.358972 processed with 18 changes in thread 11
  0:00:18.908    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_51_length_31299_cov_9.338928 processed with 17 changes in thread 6
  0:00:18.913    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_56_length_26007_cov_9.247358 processed with 13 changes in thread 4
  0:00:18.916    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_57_length_24953_cov_9.437128 processed with 17 changes in thread 15
  0:00:18.917    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_58_length_24791_cov_9.431820 processed with 5 changes in thread 1
  0:00:18.956    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_60_length_24062_cov_9.420930 processed with 7 changes in thread 2
  0:00:18.974    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_59_length_24346_cov_9.340517 processed with 6 changes in thread 7
  0:00:18.985    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_61_length_23950_cov_9.240355 processed with 14 changes in thread 9
  0:00:19.034    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_62_length_23365_cov_9.311276 processed with 3 changes in thread 13
  0:00:19.055    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_65_length_22151_cov_9.331974 processed with 4 changes in thread 10
  0:00:19.060    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_63_length_23326_cov_9.087402 processed with 7 changes in thread 12
  0:00:19.061    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_64_length_22851_cov_9.505225 processed with 13 changes in thread 3
  0:00:19.063    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_67_length_21459_cov_9.305631 processed with 9 changes in thread 5
  0:00:19.072    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_66_length_21630_cov_9.460168 processed with 7 changes in thread 0
  0:00:19.114    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_70_length_20349_cov_9.175069 processed with 15 changes in thread 11
  0:00:19.115    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_68_length_21372_cov_9.361446 processed with 4 changes in thread 14
  0:00:19.128    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_69_length_20560_cov_8.885710 processed with 20 changes in thread 8
  0:00:19.154    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_72_length_20049_cov_9.416383 processed with 1 changes in thread 4
  0:00:19.193    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_71_length_20334_cov_9.237153 processed with 18 changes in thread 6
  0:00:19.849    76M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 255)   Gluing processed contigs
  0:00:19.870    64M / 288M  INFO    General                 (main.cpp                  :  72)   Correcting time: 0 hours 0 minutes 19 seconds

== Processing of contigs


== Running contig polishing tool: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-corrector-core /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/contigs/configs/corrector.info /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta


== Dataset description file was created: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/contigs/configs/corrector.info

/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/contigs/configs/log.properties  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  58)   Starting MismatchCorrector, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  59)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 195)   Splitting assembly...
  0:00:00.001     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 196)   Assembly file: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta
  0:00:00.261     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 203)   Processing paired sublib of number 0
  0:00:00.261     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 206)   /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
  0:00:00.261     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 140)   Running bwa index ...: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta
[bwa_index] Pack FASTA... 0.07 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.40 seconds elapse.
[bwa_index] Update BWT... 0.06 sec
[bwa_index] Pack forward-only FASTA... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 0.76 sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta
[main] Real time: 2.360 sec; CPU: 2.351 sec
  0:00:02.625     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 149)   Running bwa mem ...:/home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem  -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz  > /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_ts3eej1f/lib0_xpD8b2/tmp.sam
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
[main] Real time: 9.463 sec; CPU: 90.052 sec
  0:00:12.146     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 209)   Adding samfile /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_ts3eej1f/lib0_xpD8b2/tmp.sam
  0:00:15.640    56M / 56M   INFO   DatasetProcessor         (dataset_processor.cpp     : 105)   processed 1000000reads, flushing
  0:00:16.517    20M / 60M   INFO   DatasetProcessor         (dataset_processor.cpp     : 235)   Processing contigs
  0:00:16.820    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_16_length_20142_cov_9.388886 processed with 8 changes in thread 11
  0:00:16.825    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_15_length_20345_cov_9.764210 processed with 0 changes in thread 15
  0:00:16.832    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_11_length_22641_cov_9.907818 processed with 0 changes in thread 2
  0:00:16.832    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_14_length_21372_cov_9.361446 processed with 4 changes in thread 3
  0:00:16.841    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_13_length_21930_cov_9.955384 processed with 1 changes in thread 7
  0:00:16.850    92M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_6_length_24310_cov_9.351917 processed with 6 changes in thread 1
  0:00:16.857    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_8_length_24220_cov_9.404962 processed with 5 changes in thread 4
  0:00:16.864    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_12_length_22151_cov_9.331974 processed with 3 changes in thread 14
  0:00:16.869    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_9_length_23745_cov_9.673187 processed with 5 changes in thread 5
  0:00:16.873    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_10_length_23680_cov_9.427319 processed with 6 changes in thread 8
  0:00:16.874    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_2_length_28101_cov_9.624358 processed with 7 changes in thread 0
  0:00:16.881    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_7_length_24297_cov_9.539595 processed with 6 changes in thread 13
  0:00:16.892    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_5_length_26093_cov_9.203990 processed with 6 changes in thread 6
  0:00:16.900    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_3_length_27449_cov_9.297348 processed with 4 changes in thread 9
  0:00:16.910    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_4_length_27046_cov_9.518818 processed with 5 changes in thread 10
  0:00:16.977    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_1_length_31311_cov_9.432349 processed with 0 changes in thread 12
  0:00:17.085    84M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_17_length_20131_cov_9.570460 processed with 1 changes in thread 11
  0:00:17.105    80M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_18_length_20049_cov_9.416383 processed with 1 changes in thread 15
  0:00:20.082    80M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 255)   Gluing processed contigs
  0:00:20.109    64M / 92M   INFO    General                 (main.cpp                  :  72)   Correcting time: 0 hours 0 minutes 20 seconds

===== Mismatch correction finished.

 * Assembled contigs are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/contigs.fasta
 * Assembled scaffolds are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/scaffolds.fasta
 * Assembly graph is in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/assembly_graph.fastg
 * Assembly graph in GFA format is in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/assembly_graph_with_scaffolds.gfa
 * Paths in the assembly graph corresponding to the contigs are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/scaffolds.paths

======= SPAdes pipeline finished.

SPAdes log can be found here: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/spades.log

Thank you for using SPAdes!

    -Use 16 CPU threads

    -Output is saved in SPAdes_Out directory

    MaSuRCA assembler

    • Create directory for running MaSuRCA
    In [79]:
    cd ..

    /home/annotest/AssemblyWS
    In [92]:
    mkdir MaSuRCA
  • Change directory to working directory, create symbolic links of FASTQ files.
    • In [93]:
    cd MaSuRCA

    /home/annotest/AssemblyWS/MaSuRCA
    In [94]:
    %%bash
ln -s ../FASTQ/* .
    In [95]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:28 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:28 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Generate template of the config file
    • In [96]:
    %%bash
/share/apps/MaSuRCA-3.2.8/bin/masurca -G config.txt
  • Edit the config file to specify our raw reads

    • nano config.txt

    Change the contents as follow :

  PE= pe 300 50  cabV2_read1.fq.gz  cabV2_read2.fq.gz
  #JUMP= sh 3600 200  /FULL_PATH/short_1.fastq  /FULL_PATH/short_2.fastq
    In [98]:
    cat config.txt

    # example configuration file 

# DATA is specified as type {PE,JUMP,OTHER,PACBIO} and 5 fields:
# 1)two_letter_prefix 2)mean 3)stdev 4)fastq(.gz)_fwd_reads
# 5)fastq(.gz)_rev_reads. The PE reads are always assumed to be
# innies, i.e. --->.<---, and JUMP are assumed to be outties
# <---.--->. If there are any jump libraries that are innies, such as
# longjump, specify them as JUMP and specify NEGATIVE mean. Reverse reads
# are optional for PE libraries and mandatory for JUMP libraries. Any
# OTHER sequence data (454, Sanger, Ion torrent, etc) must be first
# converted into Celera Assembler compatible .frg files (see
# http://wgs-assembler.sourceforge.com)
DATA
#Illumina paired end reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#if single-end, do not specify <reverse_reads>
#MUST HAVE Illumina paired end reads to use MaSuRCA
PE= pe 300 50  cabV2_read1.fq.gz cabV2_read2.fq.gz
#Illumina mate pair reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#JUMP= sh 3600 200  /FULL_PATH/short_1.fastq  /FULL_PATH/short_2.fastq
#pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
#if you have both types of reads supply them both as NANOPORE type
#PACBIO=/FULL_PATH/pacbio.fa
#NANOPORE=/FULL_PATH/nanopore.fa
#Other reads (Sanger, 454, etc) one frg file, concatenate your frg files into one if you have many
#OTHER=/FULL_PATH/file.frg
END

PARAMETERS
#set this to 1 if your Illumina jumping library reads are shorter than 100bp
EXTEND_JUMP_READS=0
#this is k-mer size for deBruijn graph values between 25 and 127 are supported, auto will compute the optimal size based on the read data and GC content
GRAPH_KMER_SIZE = auto
#set this to 1 for all Illumina-only assemblies
#set this to 0 if you have more than 15x coverage by long reads (Pacbio or Nanopore) or any other long reads/mate pairs (Illumina MP, Sanger, 454, etc)
USE_LINKING_MATES = 0
#specifies whether to run mega-reads correction on the grid
USE_GRID=0
#specifies queue to use when running on the grid MANDATORY
GRID_QUEUE=all.q
#batch size in the amount of long read sequence for each batch on the grid
GRID_BATCH_SIZE=300000000
#use at most this much coverage by the longest Pacbio or Nanopore reads
LHE_COVERAGE=30
#set to 1 to only do one pass of mega-reads, for faster but worse quality assembly
MEGA_READS_ONE_PASS=0
#this parameter is useful if you have too many Illumina jumping library mates. Typically set it to 60 for bacteria and 300 for the other organisms 
LIMIT_JUMP_COVERAGE = 300
#these are the additional parameters to Celera Assembler.  do not worry about performance, number or processors or batch sizes -- these are computed automatically. 
#set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other organisms.
CA_PARAMETERS =  cgwErrorRate=0.15
#minimum count k-mers used in error correction 1 means all k-mers are used.  one can increase to 2 if Illumina coverage >100
KMER_COUNT_THRESHOLD = 1
#whether to attempt to close gaps in scaffolds with Illumina data
CLOSE_GAPS=1
#auto-detected number of cpus to use
NUM_THREADS = 16
#this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*estimated_coverage
JF_SIZE = 200000000
#set this to 1 to use SOAPdenovo contigging/scaffolding module.  Assembly will be worse but will run faster. Useful for very large (>5Gbp) genomes from Illumina-only data
SOAP_ASSEMBLY=0
END
  • Generate the script file
    • In [99]:
    %%bash
/share/apps/MaSuRCA-3.2.8/bin/masurca config.txt

    Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run assembly
    In [100]:
    ls -l

    total 20
-rwxr-xr-x 1 jupyterhub1 jupyterhub1 13467 Aug  7 16:31 assemble.sh*
lrwxrwxrwx 1 jupyterhub1 jupyterhub1    26 Aug  7 16:28 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1    26 Aug  7 16:28 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
-rw-rw-r-- 1 jupyterhub1 jupyterhub1  3503 Aug  7 16:30 config.txt
  • Execute the assemble.sh script
    • In [101]:
    %%bash
./assemble.sh

    [Tue Aug  7 16:31:53 +07 2018] Processing pe library reads
[Tue Aug  7 16:31:55 +07 2018] Average PE read length 151
[Tue Aug  7 16:31:56 +07 2018] Using kmer size of 99 for the graph
[Tue Aug  7 16:31:56 +07 2018] MIN_Q_CHAR: 33
[Tue Aug  7 16:31:56 +07 2018] Creating mer database for Quorum
[Tue Aug  7 16:32:00 +07 2018] Error correct PE.
[Tue Aug  7 16:32:12 +07 2018] Estimating genome size.
[Tue Aug  7 16:32:16 +07 2018] Estimated genome size: 4694327
[Tue Aug  7 16:32:16 +07 2018] Creating k-unitigs with k=99
[Tue Aug  7 16:32:27 +07 2018] Computing super reads from PE 
[Tue Aug  7 16:32:31 +07 2018] Celera Assembler
[Tue Aug  7 16:32:32 +07 2018] ovlMerThreshold=75
[Tue Aug  7 16:33:08 +07 2018] Overlap/unitig success
[Tue Aug  7 16:33:08 +07 2018] recomputing A-stat for super-reads
[Tue Aug  7 16:33:34 +07 2018] recomputing A-stat for super-reads
[Tue Aug  7 16:33:36 +07 2018] Unitig consensus success
[Tue Aug  7 16:34:03 +07 2018] CA success
[Tue Aug  7 16:34:03 +07 2018] No gap closing possible.
[Tue Aug  7 16:34:08 +07 2018] Assembly complete, final scaffold sequences are in CA/final.genome.scf.fasta
[Tue Aug  7 16:34:08 +07 2018] All done

    =================================================================================================================

    QUAST : Quality Assessment Tool for Genome Assemblies

    Compare the quality of the assemblers

    Software is installed at /share/quast-5.0.0

    • Create directory for running QUAST
    In [102]:
    cd ..

    /home/annotest/AssemblyWS
    In [103]:
    mkdir QUAST
  • Change directory to working directory, create symbolic links of contigs files and reference file.
    • In [104]:
    cd QUAST

    /home/annotest/AssemblyWS/QUAST
    In [105]:
    %%bash
ln -s ../Velvet/Test_75/contigs.fa contigs_velvet_K75.fa
    In [106]:
    %%bash
ln -s ../VelvetOptimiser/auto_data_91/contigs.fa contigs_velvetOpt_K91.fa
    In [113]:
    %%bash
ln -s ../SPAdes/SPAdes_Out/contigs.fasta contigs_SPAdes.fa
    In [114]:
    %%bash
ln -s ../SPAdes/SPAdes_Out/scaffolds.fasta scaffolds_SPAdes.fa
    In [119]:
    %%bash
ln -s ../MaSuRCA/CA/final.genome.scf.fasta scaffolds_MaSuRCA.fa
    In [110]:
    %%bash
ln -s ../FASTA/cabV2.fa .
  • Run the QUAST
    • In [120]:
    %%bash
/share/apps/quast-5.0.0/quast.py -r cabV2.fa -t 4 contigs_velvet_K75.fa contigs_velvetOpt_K91.fa contigs_SPAdes.fa scaffolds_SPAdes.fa scaffolds_MaSuRCA.fa -o QUAST_Report

    /share/apps/quast-5.0.0/quast.py -r cabV2.fa -t 4 contigs_velvet_K75.fa contigs_velvetOpt_K91.fa contigs_SPAdes.fa scaffolds_SPAdes.fa scaffolds_MaSuRCA.fa -o QUAST_Report

Version: 5.0.0

System information:
  OS: Linux-3.10.0-514.26.2.el7.x86_64-x86_64-with-centos-7.4.1708-Core (linux_64)
  Python version: 3.5.5
  CPUs number: 144

Started: 2018-08-07 16:40:51

Logging to /home/annotest/AssemblyWS/QUAST/QUAST_Report/quast.log

CWD: /home/annotest/AssemblyWS/QUAST
Main parameters: 
  MODE: default, threads: 4, minimum contig length: 500, minimum alignment length: 65, \
  ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /home/annotest/AssemblyWS/QUAST/cabV2.fa ==> cabV2

Contigs:
  Pre-processing...
  1  contigs_velvet_K75.fa ==> contigs_velvet_K75
  2  contigs_velvetOpt_K91.fa ==> contigs_velvetOpt_K91
  3  contigs_SPAdes.fa ==> contigs_SPAdes
  4  scaffolds_SPAdes.fa ==> scaffolds_SPAdes
  5  scaffolds_MaSuRCA.fa ==> scaffolds_MaSuRCA

2018-08-07 16:40:56
Running Basic statistics processor...
  Reference genome:
    cabV2.fa, length = 4799920, num fragments = 1, GC % = 31.97
  Contig files: 
    1  contigs_velvet_K75
    2  contigs_velvetOpt_K91
    3  contigs_SPAdes
    4  scaffolds_SPAdes
    5  scaffolds_MaSuRCA
  Calculating N50 and L50...
    1  contigs_velvet_K75, N50 = 55329, L50 = 25, Total length = 4591890, GC % = 31.99, # N's per 100 kbp =  441.80
    2  contigs_velvetOpt_K91, N50 = 22892, L50 = 57, Total length = 4615405, GC % = 31.99, # N's per 100 kbp =  1012.61
    3  contigs_SPAdes, N50 = 8046, L50 = 171, Total length = 4589773, GC % = 31.98, # N's per 100 kbp =  0.00
    4  scaffolds_SPAdes, N50 = 49269, L50 = 29, Total length = 4644726, GC % = 31.99, # N's per 100 kbp =  1160.89
    5  scaffolds_MaSuRCA, N50 = 63511, L50 = 20, Total length = 4615776, GC % = 32.01, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/GC_content_plot.pdf
  Drawing contigs_velvet_K75 GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvet_K75_GC_content_plot.pdf
  Drawing contigs_velvetOpt_K91 GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvetOpt_K91_GC_content_plot.pdf
  Drawing contigs_SPAdes GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_SPAdes_GC_content_plot.pdf
  Drawing scaffolds_SPAdes GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/scaffolds_SPAdes_GC_content_plot.pdf
  Drawing scaffolds_MaSuRCA GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/scaffolds_MaSuRCA_GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/coverage_histogram.pdf
  Drawing contigs_velvet_K75 coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvet_K75_coverage_histogram.pdf
  Drawing contigs_velvetOpt_K91 coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvetOpt_K91_coverage_histogram.pdf
  Drawing contigs_SPAdes coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_SPAdes_coverage_histogram.pdf
  Drawing scaffolds_SPAdes coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/scaffolds_SPAdes_coverage_histogram.pdf
Done.

2018-08-07 16:41:01
Running Contig analyzer...
  1  contigs_velvet_K75
  1  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_contigs_velvet_K75.stdout and contigs_report_contigs_velvet_K75.stderr...
  1  Aligning contigs to the reference
  2  contigs_velvetOpt_K91
  2  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_contigs_velvetOpt_K91.stdout and contigs_report_contigs_velvetOpt_K91.stderr...
  2  Aligning contigs to the reference
  3  contigs_SPAdes
  3  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_contigs_SPAdes.stdout and contigs_report_contigs_SPAdes.stderr...
  3  Aligning contigs to the reference
  4  scaffolds_SPAdes
  4  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_scaffolds_SPAdes.stdout and contigs_report_scaffolds_SPAdes.stderr...
  4  Aligning contigs to the reference
  1  Analysis is finished.
  5  scaffolds_MaSuRCA
  5  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_scaffolds_MaSuRCA.stdout and contigs_report_scaffolds_MaSuRCA.stderr...
  5  Aligning contigs to the reference
  3  Analysis is finished.
  2  Analysis is finished.
  4  Analysis is finished.
  5  Analysis is finished.
  Creating total report...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/misassemblies_plot.pdf
  Drawing misassemblies FRCurve plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/misassemblies_frcurve_plot.pdf
Done.

2018-08-07 16:41:08
Running NA-NGA calculation...
  1  contigs_velvet_K75, Largest alignment = 171055, NA50 = 44603, NGA50 = 43734, LA50 = 27, LGA50 = 29
  2  contigs_velvetOpt_K91, Largest alignment = 112338, NA50 = 20897, NGA50 = 19883, LA50 = 58, LGA50 = 63
  3  contigs_SPAdes, Largest alignment = 31311, NA50 = 8044, NGA50 = 7841, LA50 = 171, LGA50 = 185
  4  scaffolds_SPAdes, Largest alignment = 139088, NA50 = 44026, NGA50 = 42900, LA50 = 31, LGA50 = 33
  5  scaffolds_MaSuRCA, Largest alignment = 219320, NA50 = 63511, NGA50 = 62173, LA50 = 20, LGA50 = 22
  Drawing cumulative plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/aligned_stats/NGAx_plot.pdf
Done.

2018-08-07 16:41:09
Running Genome analyzer...
  NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.

  NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
  1  contigs_velvet_K75
  2  contigs_velvetOpt_K91
  3  contigs_SPAdes
  4  scaffolds_SPAdes
  1  Analysis is finished.
  5  scaffolds_MaSuRCA
  2  Analysis is finished.
  3  Analysis is finished.
  4  Analysis is finished.
  5  Analysis is finished.
  Drawing Genome fraction, % histogram...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/genome_stats/genome_fraction_histogram.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2018-08-07 16:41:13
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2018-08-07 16:41:18
RESULTS:
  Text versions of total report are saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/report.html
  PDF version (tables and plots) is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/report.pdf
  Icarus (contig browser) is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/icarus.html
  Log is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/quast.log

Finished: 2018-08-07 16:41:18
Elapsed time: 0:00:26.266695
NOTICEs: 3; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using QUAST!

    The report is generated in QUAST_Report directory.

  • Use ~/public_html to visualize the QUAST report
    • In [ ]:
    cd ~/public_html
    In [124]:
    cp -rp ../AssemblyWS/QUAST/QUAST_Report .
    In [125]:
    ls -l

    total 16
-rwxr-xr-x  1 annotest    annotest     151 Aug  1 02:48 index.html*
drwxrwxr-x 11 annotest    annotest    4096 Aug  1 03:10 JBrowse/
drwxrwxr-x  7 jupyterhub1 jupyterhub1 4096 Aug  7 16:41 QUAST_Report/
drwxrwxr-x  3 annotest    annotest    4096 Aug  6 21:33 Tomato/
  • Use your Web browser to visualize the QUAST report
    • In [ ]:
    http://breedserve.cab.kps.ku.ac.th/~annotest/QUAST_Report/report.html

    change ~annotest to your username

    In [126]:
    from IPython.display import HTML
HTML(filename="/home/annotest/public_html/QUAST_Report/report.html")
    Out[126]:

    QUAST

    Quality Assessment Tool for Genome Assemblies by CAB

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    {{ qualities }}
    {{ mainMetrics }}
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