ursky
commented
5 years ago I need to see the complete unedited output of metawrap to help you.
Open xiaochen2015 opened 5 years ago
ursky
commented
5 years ago I need to see the complete unedited output of metawrap to help you.
xiaochen2015
commented
5 years ago thank you for you replay!
I used this order: metawrap binning -o INITIAL_BINNING -t 40 -a ASSEMBLY_test/final_assembly.fasta --metabat2 --maxbin2 --concoct --run-checkm CLEAN_READS_test/ERR*fastq
The files in folder "INITIAL_BINNING" as follow:
concoct_bins concoct_bins.checkm maxbin2_bins maxbin2_bins.checkm metabat2_bins
metabat2_bins.checkm work_files
concoct_bins.stats maxbin2_bins.stats metabat2_bins.stats.**The process information of output of this order were 2 files (file1: metawrap_bin_sop_test.sh.o) .File1 was as follow:
**
/home/*********/Work_space/metawrap_sample
metawrap binning -o INITIAL_BINNING -t 40 -a ASSEMBLY_test/final_assembly.fasta --metabat2 --maxbin2 --concoct --run-checkm CLEAN_READS_test/ERR011347_1.fastq CLEAN_READS_test/ERR011347_2.fastq CLEAN_READS_test/ERR011348_1.fastq CLEAN_READS_test/ERR011348_2.fastq CLEAN_READS_test/ERR011349_1.fastq CLEAN_READS_test/ERR011349_2.fastq
------------------------------------------------------------------------------------------------------------------------
----- Entered read type: paired -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- 3 forward and 3 reverse read files detected -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### ALIGNING READS TO MAKE COVERAGE FILES #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making copy of assembly file ASSEMBLY_test/final_assembly.fasta -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Indexing assembly file -----
------------------------------------------------------------------------------------------------------------------------
[bwt_gen] Finished constructing BWT in 35 iterations.
------------------------------------------------------------------------------------------------------------------------
----- Aligning CLEAN_READS_test/ERR011347_1.fastq and CLEAN_READS_test/ERR011347_2.fastq back -----
----- to assembly, sorting the alignment, and gathering statistics on insert lengths -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Aligning CLEAN_READS_test/ERR011348_1.fastq and CLEAN_READS_test/ERR011348_2.fastq back -----
----- to assembly, sorting the alignment, and gathering statistics on insert lengths -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Aligning CLEAN_READS_test/ERR011349_1.fastq and CLEAN_READS_test/ERR011349_2.fastq back -----
----- to assembly, sorting the alignment, and gathering statistics on insert lengths -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### RUNNING METABAT2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Starting binning with metaBAT2... -----
------------------------------------------------------------------------------------------------------------------------
MetaBAT 2 (v2.12.1) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200.
19 bins (23698278 bases in total) formed.
------------------------------------------------------------------------------------------------------------------------
----- metaBAT2 finished successfully, and found 20 bins! -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Running CheckM on INITIAL_BINNING/metabat2_bins bins -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- There is 4 RAM and 40 threads available, and each pplacer thread uses <40GB, so I will -----
----- use 0 threads for pplacer -----
------------------------------------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
bin.10 o__Clostridiales (UID1212) 172 263 149 12 249 2 0 0 0 98.58 0.81 0.00
bin.unbinned k__Bacteria (UID203) 5449 103 57 2 2 10 15 16 58 97.37 351.58 2.66
bin.14 o__Clostridiales (UID1212) 172 263 149 60 202 1 0 0 0 84.90 0.22 100.00
bin.5 p__Euryarchaeota (UID3) 148 188 125 25 155 8 0 0 0 84.53 1.59 0.00
bin.17 o__Bacteroidales (UID2657) 160 492 269 142 345 5 0 0 0 75.63 0.85 40.00
bin.13 k__Bacteria (UID203) 5449 103 57 20 53 28 2 0 0 74.24 21.61 5.88
bin.19 o__Clostridiales (UID1212) 172 263 149 54 207 2 0 0 0 74.07 0.40 50.00
bin.4 o__Clostridiales (UID1212) 172 263 149 124 132 7 0 0 0 47.25 3.02 42.86
bin.6 k__Bacteria (UID203) 5449 103 57 74 19 8 2 0 0 44.44 15.79 14.29
bin.9 k__Bacteria (UID203) 5449 104 58 70 34 0 0 0 0 43.44 0.00 0.00
bin.11 k__Bacteria (UID203) 5449 103 57 76 26 1 0 0 0 37.02 0.88 100.00
bin.8 k__Bacteria (UID203) 5449 104 58 82 20 2 0 0 0 32.21 2.59 50.00
bin.2 o__Selenomonadales (UID1024) 64 334 167 241 91 2 0 0 0 30.55 0.35 50.00
bin.3 k__Bacteria (UID203) 5449 104 58 87 17 0 0 0 0 18.73 0.00 0.00
bin.1 k__Bacteria (UID203) 5449 104 58 91 13 0 0 0 0 17.24 0.00 0.00
bin.15 root (UID1) 5656 56 24 55 1 0 0 0 0 4.17 0.00 0.00
bin.7 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.18 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.16 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.12 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- There are 5 'good' bins found in INITIAL_BINNING/metabat2_bins! (>70% completion and <10% -----
----- contamination) -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### RUNNING MAXBIN2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- split master contig depth file into individual files for maxbin2 input -----
------------------------------------------------------------------------------------------------------------------------
processing ERR011347.bam depth file...
processing ERR011348.bam depth file...
processing ERR011349.bam depth file...
MaxBin 2.2.4
No Contig file. Please specify contig file by -contig
MaxBin - a metagenomics binning software.
Usage:
run_MaxBin.pl
-contig (contig file)
-out (output file)
(Input reads and abundance information)
[-reads (reads file) -reads2 (readsfile) -reads3 (readsfile) -reads4 ... ]
[-abund (abundance file) -abund2 (abundfile) -abund3 (abundfile) -abund4 ... ]
(You can also input lists consisting of reads and abundance files)
[-reads_list (list of reads files)]
[-abund_list (list of abundance files)]
(Other parameters)
[-min_contig_length (minimum contig length. Default 1000)]
[-max_iteration (maximum Expectation-Maximization algorithm iteration number. Default 50)]
[-thread (thread num; default 1)]
[-prob_threshold (probability threshold for EM final classification. Default 0.9)]
[-plotmarker]
[-markerset (marker gene sets, 107 (default) or 40. See README for more information.)]
(for debug purpose)
[-version] [-v] (print version number)
[-verbose]
[-preserve_intermediate]
Please specify either -reads or -abund information.
You can input multiple reads and/or abundance files at the same time.
Please read README file for more details.
------------------------------------------------------------------------------------------------------------------------
----- Starting binning with MaxBin2... -----
------------------------------------------------------------------------------------------------------------------------
MaxBin 2.2.4
Input contig: INITIAL_BINNING/work_files/assembly.fa
Thread: 40
Min contig length: 1000
out header: INITIAL_BINNING/work_files/maxbin2_out/bin
Located abundance file [/home/*********/Work_space/metawrap_sample/INITIAL_BINNING/work_files/mb2_ERR011347.txt]
Located abundance file [/home/*********/Work_space/metawrap_sample/INITIAL_BINNING/work_files/mb2_ERR011348.txt]
Located abundance file [/home/*********/Work_space/metawrap_sample/INITIAL_BINNING/work_files/mb2_ERR011349.txt]
Searching against 107 marker genes to find starting seed contigs for [INITIAL_BINNING/work_files/assembly.fa]...
Running FragGeneScan....
Running HMMER hmmsearch....
Done data collection. Running MaxBin...
Command: /home/*********/anaconda2/envs/metawrap/bin/src/MaxBin -fasta INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp -abund INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund1 -abund2 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund2 -abund3 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund3 -seed INITIAL_BINNING/work_files/maxbin2_out/bin.seed -out INITIAL_BINNING/work_files/maxbin2_out/bin -min_contig_length 1000 -thread 40
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_10193_length_27026_cov_24.0000 [0.031405] [0.022028] [45.676500]
k93_85582_length_21473_cov_23.0000 [18.398700] [24.175600] [0.056104]
k93_29896_length_5559_cov_7.0000 [7.725280] [4.920410] [0.251507]
k93_5833_length_4790_cov_7.0000 [7.736920] [3.476300] [0.021250]
k93_66574_length_3474_cov_13.0000 [3.465450] [8.213180] [14.746300]
k93_45381_length_1750_cov_7.0000 [7.072200] [4.504870] [0.947179]
k93_55421_length_1670_cov_11.0000 [7.454490] [6.797950] [6.271120]
k93_79885_length_1254_cov_7.0000 [5.592620] [6.443380] [0.000100]
k93_100915_length_1230_cov_11.0000 [12.465000] [10.059600] [0.000100]
k93_20974_length_1178_cov_8.0000 [3.466060] [11.175400] [2.671850]
Get 10 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
Iteration 24
Iteration 25
Iteration 26
Iteration 27
Iteration 28
Iteration 29
Iteration 30
Iteration 31
Iteration 32
Iteration 33
Iteration 34
Iteration 35
Iteration 36
Iteration 37
Iteration 38
Iteration 39
Iteration 40
Iteration 41
Iteration 42
Iteration 43
Iteration 44
Iteration 45
Iteration 46
Iteration 47
Iteration 48
Iteration 49
Iteration 50
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 135 (0.71%)
Elapsed time: 0 days 00:01:41
Done data collection. Running MaxBin...
Command: /home/*********/anaconda2/envs/metawrap/bin/src/MaxBin -fasta INITIAL_BINNING/work_files/maxbin2_out/bin.0001.fasta -abund INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund1 -abund2 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund2 -abund3 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund3 -seed INITIAL_BINNING/work_files/maxbin2_out/bin.0001.out.seed -out INITIAL_BINNING/work_files/maxbin2_out/bin.0001.out -min_contig_length 1000 -thread 40
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_100292_length_15776_cov_23.0000 [0.019633] [0.005488] [42.932100]
k93_24693_length_7817_cov_35.0000 [0.078018] [0.009208] [69.611700]
Get 2 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time: 0 days 00:00:01
Done data collection. Running MaxBin...
Command: /home/*********/anaconda2/envs/metawrap/bin/src/MaxBin -fasta INITIAL_BINNING/work_files/maxbin2_out/bin.0004.fasta -abund INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund1 -abund2 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund2 -abund3 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund3 -seed INITIAL_BINNING/work_files/maxbin2_out/bin.0004.out.seed -out INITIAL_BINNING/work_files/maxbin2_out/bin.0004.out -min_contig_length 1000 -thread 40
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_29480_length_2818_cov_6.0000 [7.761540] [2.377580] [0.000100]
k93_98585_length_1146_cov_5.0000 [6.172970] [2.214420] [0.530132]
Get 2 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time: 0 days 00:00:03
Done data collection. Running MaxBin...
Command: /home/*********/anaconda2/envs/metawrap/bin/src/MaxBin -fasta INITIAL_BINNING/work_files/maxbin2_out/bin.0008.fasta -abund INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund1 -abund2 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund2 -abund3 INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund3 -seed INITIAL_BINNING/work_files/maxbin2_out/bin.0008.out.seed -out INITIAL_BINNING/work_files/maxbin2_out/bin.0008.out -min_contig_length 1000 -thread 40
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_9639_length_2457_cov_12.0000 [6.342760] [10.634200] [0.395702]
k93_53787_length_1176_cov_6.0000 [2.619490] [7.163550] [1.909340]
Get 2 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
Iteration 24
Iteration 25
Iteration 26
Iteration 27
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time: 0 days 00:00:06
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_10193_length_27026_cov_24.0000 [0.031405] [0.022028] [45.676500]
k93_85582_length_21473_cov_23.0000 [18.398700] [24.175600] [0.056104]
k93_29896_length_5559_cov_7.0000 [7.725280] [4.920410] [0.251507]
k93_5833_length_4790_cov_7.0000 [7.736920] [3.476300] [0.021250]
k93_66574_length_3474_cov_13.0000 [3.465450] [8.213180] [14.746300]
k93_45381_length_1750_cov_7.0000 [7.072200] [4.504870] [0.947179]
k93_55421_length_1670_cov_11.0000 [7.454490] [6.797950] [6.271120]
k93_79885_length_1254_cov_7.0000 [5.592620] [6.443380] [0.000100]
k93_100915_length_1230_cov_11.0000 [12.465000] [10.059600] [0.000100]
k93_20974_length_1178_cov_8.0000 [3.466060] [11.175400] [2.671850]
Get 10 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
Iteration 24
Iteration 25
Iteration 26
Iteration 27
Iteration 28
Iteration 29
Iteration 30
Iteration 31
Iteration 32
Iteration 33
Iteration 34
Iteration 35
Iteration 36
Iteration 37
Iteration 38
Iteration 39
Iteration 40
Iteration 41
Iteration 42
Iteration 43
Iteration 44
Iteration 45
Iteration 46
Iteration 47
Iteration 48
Iteration 49
Iteration 50
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 135 (0.71%)
Elapsed time: 0 days 00:01:41
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_100292_length_15776_cov_23.0000 [0.019633] [0.005488] [42.932100]
k93_24693_length_7817_cov_35.0000 [0.078018] [0.009208] [69.611700]
Get 2 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time: 0 days 00:00:01
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_29480_length_2818_cov_6.0000 [7.761540] [2.377580] [0.000100]
k93_98585_length_1146_cov_5.0000 [6.172970] [2.214420] [0.530132]
Get 2 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time: 0 days 00:00:03
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
k93_9639_length_2457_cov_12.0000 [6.342760] [10.634200] [0.395702]
k93_53787_length_1176_cov_6.0000 [2.619490] [7.163550] [1.909340]
Get 2 seeds.
Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13
Iteration 14
Iteration 15
Iteration 16
Iteration 17
Iteration 18
Iteration 19
Iteration 20
Iteration 21
Iteration 22
Iteration 23
Iteration 24
Iteration 25
Iteration 26
Iteration 27
EM finishes successfully.
Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time: 0 days 00:00:06
bin.002.marker.fasta
bin.003.marker.fasta
bin.004.marker.fasta
bin.005.marker.fasta
bin.006.marker.fasta
bin.007.marker.fasta
bin.008.marker.fasta
bin.009.marker.fasta
bin.010.marker.fasta
bin.011.marker.fasta
bin.012.marker.fasta
bin.013.marker.fasta
Deleting intermediate files.
========== Job finished ==========
Yielded 13 bins for contig (scaffold) file INITIAL_BINNING/work_files/assembly.fa
Here are the output files for this run.
Please refer to the README file for further details.
Summary file: INITIAL_BINNING/work_files/maxbin2_out/bin.summary
Genome abundance info file: INITIAL_BINNING/work_files/maxbin2_out/bin.abundance
Marker counts: INITIAL_BINNING/work_files/maxbin2_out/bin.marker
Marker genes for each bin: INITIAL_BINNING/work_files/maxbin2_out/bin.marker_of_each_gene.tar.gz
Bin files: INITIAL_BINNING/work_files/maxbin2_out/bin.001.fasta - INITIAL_BINNING/work_files/maxbin2_out/bin.013.fasta
Unbinned sequences: INITIAL_BINNING/work_files/maxbin2_out/bin.noclass
========== Elapsed Time ==========
0 hours 2 minutes and 16 seconds.
------------------------------------------------------------------------------------------------------------------------
----- MaxBin2 finished successfully, and found 13 bins! -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Running CheckM on INITIAL_BINNING/maxbin2_bins bins -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- There is 4 RAM and 40 threads available, and each pplacer thread uses <40GB, so I will -----
----- use 0 threads for pplacer -----
------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
bin.1 o__Clostridiales (UID1212) 172 263 149 2 244 17 0 0 0 99.11 4.39 5.88
bin.12 o__Clostridiales (UID1212) 172 263 149 27 229 7 0 0 0 92.19 2.69 42.86
bin.4 k__Archaea (UID2) 207 149 107 16 102 24 6 1 0 89.03 24.44 2.08
bin.3 k__Bacteria (UID203) 5449 104 58 19 40 28 13 4 0 80.77 56.26 15.38
bin.9 k__Bacteria (UID203) 5449 103 57 43 26 16 10 8 0 76.33 76.75 15.96
bin.11 o__Clostridiales (UID1212) 172 263 149 52 202 9 0 0 0 75.42 1.08 11.11
bin.2 o__Clostridiales (UID1212) 172 263 149 73 111 74 5 0 0 72.83 34.97 7.87
bin.10 o__Clostridiales (UID1212) 172 263 149 72 174 15 2 0 0 68.89 9.23 14.29
bin.5 k__Bacteria (UID203) 5449 103 57 59 30 11 2 0 1 66.37 27.19 7.41
bin.6 k__Bacteria (UID203) 5449 103 57 24 32 25 18 4 0 64.59 50.38 3.88
bin.7 o__Clostridiales (UID1120) 304 250 143 111 114 20 5 0 0 56.67 12.08 2.86
bin.8 k__Bacteria (UID2982) 88 229 147 113 81 25 9 1 0 48.67 20.79 5.17
bin.0 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- There are 3 'good' bins found in INITIAL_BINNING/maxbin2_bins! (>70% completion and <10% -----
----- contamination) -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### RUNNING CONCOCT #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Starting binning with CONCOCT. This may take a while... -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- splitting contigs into bins -----
------------------------------------------------------------------------------------------------------------------------
Loading in the bins that the contigs belong to...
Going through the entire assembly and splitting contigs into their respective bin file...
Done!
------------------------------------------------------------------------------------------------------------------------
----- CONCOCT finished successfully, and found 38 bins! -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Running CheckM on INITIAL_BINNING/concoct_bins bins -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- There is 4 RAM and 40 threads available, and each pplacer thread uses <40GB, so I will -----
----- use 0 threads for pplacer -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
bin.6 o__Clostridiales (UID1212) 172 263 149 5 253 5 0 0 0 98.92 1.87 20.00
bin.28 p__Euryarchaeota (UID3) 148 188 125 10 177 1 0 0 0 93.73 0.80 0.00
bin.35 k__Bacteria (UID203) 5449 103 57 9 30 59 4 1 0 87.40 57.76 6.49
bin.23 o__Clostridiales (UID1212) 172 263 149 62 199 2 0 0 0 83.12 0.56 50.00
bin.22 k__Bacteria (UID203) 5449 103 57 44 25 20 6 7 1 75.72 83.32 11.11
bin.3 o__Clostridiales (UID1212) 172 263 149 54 207 2 0 0 0 74.07 0.40 50.00
bin.21 o__Clostridiales (UID1212) 172 263 149 74 183 6 0 0 0 68.50 2.68 50.00
bin.32 o__Clostridiales (UID1212) 172 263 149 108 148 7 0 0 0 59.71 3.10 71.43
bin.9 k__Bacteria (UID203) 5449 104 58 60 31 11 2 0 0 57.68 21.55 23.53
bin.29 o__Selenomonadales (UID1024) 64 334 167 124 200 9 1 0 0 54.73 2.61 25.00
bin.31 o__Bacteroidales (UID2657) 160 492 269 228 219 40 5 0 0 54.20 9.42 27.27
bin.0 o__Clostridiales (UID1226) 155 278 158 140 90 37 10 1 0 46.98 20.20 5.48
bin.4 o__Bacteroidales (UID2657) 160 491 268 299 187 4 1 0 0 39.57 1.15 28.57
bin.16 k__Bacteria (UID2982) 88 229 147 154 75 0 0 0 0 34.99 0.00 0.00
bin.27 k__Bacteria (UID203) 5449 104 58 78 26 0 0 0 0 33.62 0.00 0.00
bin.14 k__Bacteria (UID203) 5449 103 57 85 18 0 0 0 0 21.69 0.00 0.00
bin.24 k__Bacteria (UID203) 5449 104 58 84 20 0 0 0 0 16.97 0.00 0.00
bin.8 k__Bacteria (UID203) 5449 103 57 90 11 2 0 0 0 15.22 3.51 50.00
bin.30 p__Bacteroidetes (UID2605) 350 314 208 257 55 2 0 0 0 13.85 0.05 50.00
bin.26 k__Bacteria (UID203) 5449 103 57 87 16 0 0 0 0 8.77 0.00 0.00
bin.1 k__Bacteria (UID203) 5449 104 58 99 5 0 0 0 0 8.62 0.00 0.00
bin.20 root (UID1) 5656 56 24 55 1 0 0 0 0 4.17 0.00 0.00
bin.33 k__Bacteria (UID203) 5449 103 57 95 8 0 0 0 0 3.43 0.00 0.00
bin.34 k__Bacteria (UID203) 5449 104 58 101 3 0 0 0 0 0.47 0.00 0.00
unbinned root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.7 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.5 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.36 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.25 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.2 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.19 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.18 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.17 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.15 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.13 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.12 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.11 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
bin.10 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- There are 4 'good' bins found in INITIAL_BINNING/concoct_bins! (>70% completion and <10% -----
----- contamination) -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### BINNING PIPELINE SUCCESSFULLY FINISHED!!! #####
########################################################################################################################And the another output file (file2: metawrap_bin_sop_test.sh.e) . File2 was as follow:
[bwa_index] Pack FASTA... 0.37 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=85978808, availableWord=18049488
[BWTIncConstructFromPacked] 10 iterations done. 29772824 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 55001224 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 77420264 characters processed.
[bwa_index] 20.65 seconds elapse.
[bwa_index] Update BWT... 0.27 sec
[bwa_index] Pack forward-only FASTA... 0.22 sec
[bwa_index] Construct SA from BWT and Occ... 7.15 sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa index INITIAL_BINNING/work_files/assembly.fa
[main] Real time: 29.762 sec; CPU: 28.663 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 9619092 sequences (400000026 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (90, 1701588, 178, 54)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (39, 70, 115)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 267)
[M::mem_pestat] mean and std.dev: (66.97, 45.29)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 343)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (121, 125, 129)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (105, 145)
[M::mem_pestat] mean and std.dev: (125.28, 6.10)
[M::mem_pestat] low and high boundaries for proper pairs: (97, 153)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (96, 1013, 1629)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4695)
[M::mem_pestat] mean and std.dev: (869.24, 988.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6228)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (67, 90, 115)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 211)
[M::mem_pestat] mean and std.dev: (77.21, 31.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 259)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 9619092 reads in 403.074 CPU sec, 13.853 real sec
[M::process] read 8900244 sequences (400000054 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (83, 1603475, 139, 66)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (40, 61, 90)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 190)
[M::mem_pestat] mean and std.dev: (59.99, 30.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 240)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (121, 125, 129)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (105, 145)
[M::mem_pestat] mean and std.dev: (125.34, 6.11)
[M::mem_pestat] low and high boundaries for proper pairs: (97, 153)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (129, 799, 1722)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4908)
[M::mem_pestat] mean and std.dev: (1016.06, 1215.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6501)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (57, 87, 241)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (94.33, 73.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 793)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 8900244 reads in 411.751 CPU sec, 13.727 real sec
[M::process] read 5569480 sequences (229832112 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (47, 948820, 85, 25)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (40, 69, 85)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 175)
[M::mem_pestat] mean and std.dev: (57.05, 24.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 220)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (121, 125, 129)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (105, 145)
[M::mem_pestat] mean and std.dev: (125.25, 6.09)
[M::mem_pestat] low and high boundaries for proper pairs: (97, 153)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (128, 1285, 4712)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13880)
[M::mem_pestat] mean and std.dev: (2124.00, 2188.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 18464)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (66, 182, 1072)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3084)
[M::mem_pestat] mean and std.dev: (579.28, 782.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4090)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 5569480 reads in 234.319 CPU sec, 6.821 real sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa mem -t 40 INITIAL_BINNING/work_files/assembly.fa CLEAN_READS_test/ERR011347_1.fastq CLEAN_READS_test/ERR011347_2.fastq
[main] Real time: 71.736 sec; CPU: 1072.169 sec
[bam_sort_core] merging from 0 files and 40 in-memory blocks...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 7897866 sequences (400000005 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (288, 1173076, 449, 84)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (90, 173, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 654)
[M::mem_pestat] mean and std.dev: (157.21, 91.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 842)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (342, 348, 354)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (318, 378)
[M::mem_pestat] mean and std.dev: (347.96, 8.74)
[M::mem_pestat] low and high boundaries for proper pairs: (306, 390)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (935, 3284, 4630)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12020)
[M::mem_pestat] mean and std.dev: (2846.76, 1956.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 15715)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 1045, 2642)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7322)
[M::mem_pestat] mean and std.dev: (1361.08, 1192.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9662)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 7897866 reads in 397.314 CPU sec, 13.645 real sec
[M::process] read 7913994 sequences (400000027 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (196, 1186369, 432, 74)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (98, 219, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 677)
[M::mem_pestat] mean and std.dev: (181.78, 115.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 870)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (342, 348, 354)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (318, 378)
[M::mem_pestat] mean and std.dev: (347.95, 8.72)
[M::mem_pestat] low and high boundaries for proper pairs: (306, 390)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1073, 3793, 4631)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11747)
[M::mem_pestat] mean and std.dev: (3005.05, 1962.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 15305)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (277, 1332, 2638)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7360)
[M::mem_pestat] mean and std.dev: (1365.03, 1194.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9721)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 7913994 reads in 403.870 CPU sec, 13.116 real sec
[M::process] read 5065398 sequences (248752085 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (173, 753814, 289, 55)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (80, 130, 246)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 578)
[M::mem_pestat] mean and std.dev: (144.76, 86.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 744)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (342, 348, 354)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (318, 378)
[M::mem_pestat] mean and std.dev: (347.93, 8.73)
[M::mem_pestat] low and high boundaries for proper pairs: (306, 390)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (952, 2923, 4629)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11983)
[M::mem_pestat] mean and std.dev: (2877.49, 1937.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 15660)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (314, 1369, 2645)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7307)
[M::mem_pestat] mean and std.dev: (1492.13, 1184.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9638)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 5065398 reads in 251.687 CPU sec, 7.195 real sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa mem -t 40 INITIAL_BINNING/work_files/assembly.fa CLEAN_READS_test/ERR011348_1.fastq CLEAN_READS_test/ERR011348_2.fastq
[main] Real time: 67.432 sec; CPU: 1074.119 sec
[bam_sort_core] merging from 0 files and 40 in-memory blocks...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 10360772 sequences (400000030 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (86, 1417917, 146, 39)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (37, 65, 107)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 247)
[M::mem_pestat] mean and std.dev: (62.43, 35.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 317)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (122, 127, 131)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (104, 149)
[M::mem_pestat] mean and std.dev: (126.70, 6.92)
[M::mem_pestat] low and high boundaries for proper pairs: (95, 158)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (15, 900, 2609)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7797)
[M::mem_pestat] mean and std.dev: (1738.25, 1938.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10391)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (72, 99, 147)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 297)
[M::mem_pestat] mean and std.dev: (85.58, 49.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 372)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 10360772 reads in 396.590 CPU sec, 13.843 real sec
[M::process] read 10219528 sequences (400000038 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (97, 1370507, 141, 46)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (37, 62, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 286)
[M::mem_pestat] mean and std.dev: (70.38, 52.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 369)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (122, 127, 131)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (104, 149)
[M::mem_pestat] mean and std.dev: (126.72, 6.92)
[M::mem_pestat] low and high boundaries for proper pairs: (95, 158)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (71, 1061, 2998)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8852)
[M::mem_pestat] mean and std.dev: (1877.71, 1966.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 11779)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (81, 103, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 636)
[M::mem_pestat] mean and std.dev: (109.56, 76.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 821)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 10219528 reads in 397.940 CPU sec, 13.253 real sec
[M::process] read 2305576 sequences (84479514 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (32, 313817, 33, 7)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (42, 56, 190)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 486)
[M::mem_pestat] mean and std.dev: (55.12, 36.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 634)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (122, 127, 131)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (104, 149)
[M::mem_pestat] mean and std.dev: (126.57, 6.91)
[M::mem_pestat] low and high boundaries for proper pairs: (95, 158)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (13, 94, 2613)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7813)
[M::mem_pestat] mean and std.dev: (1550.39, 2023.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10413)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 2305576 reads in 86.596 CPU sec, 2.655 real sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa mem -t 40 INITIAL_BINNING/work_files/assembly.fa CLEAN_READS_test/ERR011349_1.fastq CLEAN_READS_test/ERR011349_2.fastq
[main] Real time: 65.103 sec; CPU: 902.461 sec
[bam_sort_core] merging from 0 files and 40 in-memory blocks...
Output depth matrix to INITIAL_BINNING/work_files/metabat_depth.txt
Output matrix to INITIAL_BINNING/work_files/metabat_depth.txt
Opening 3 bams
Consolidating headers
Processing bam files
Thread 2 finished: ERR011349.bam with 22886298 reads and 6744748 readsWellMapped
Thread 1 finished: ERR011348.bam with 20878028 reads and 6998908 readsWellMapped
Thread 0 finished: ERR011347.bam with 24089298 reads and 9022106 readsWellMapped
Creating depth matrix file: INITIAL_BINNING/work_files/metabat_depth.txt
Closing most bam files
Closing last bam file
Finished
*******************************************************************************
[CheckM - tree] Placing bins in reference genome tree.
*******************************************************************************
Identifying marker genes in 20 bins with 40 threads:
Finished processing 0 of 20 (0.00%) bins.
Finished processing 1 of 20 (5.00%) bins.
Finished processing 2 of 20 (10.00%) bins.
Finished processing 3 of 20 (15.00%) bins.
Finished processing 4 of 20 (20.00%) bins.
Finished processing 5 of 20 (25.00%) bins.
Finished processing 6 of 20 (30.00%) bins.
Finished processing 7 of 20 (35.00%) bins.
Finished processing 8 of 20 (40.00%) bins.
Finished processing 9 of 20 (45.00%) bins.
Finished processing 10 of 20 (50.00%) bins.
Finished processing 11 of 20 (55.00%) bins.
Finished processing 12 of 20 (60.00%) bins.
Finished processing 13 of 20 (65.00%) bins.
Finished processing 14 of 20 (70.00%) bins.
Finished processing 15 of 20 (75.00%) bins.
Finished processing 16 of 20 (80.00%) bins.
Finished processing 17 of 20 (85.00%) bins.
Finished processing 18 of 20 (90.00%) bins.
Finished processing 19 of 20 (95.00%) bins.
Finished processing 20 of 20 (100.00%) bins.
Traceback (most recent call last):
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 274, in _run_finalizers
finalizer()
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 207, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'INITIAL_BINNING/metabat2_bins.tmp/pymp-WQojLO/.nfs000000000011e10d00001e15'
Saving HMM info to file.
Calculating genome statistics for 20 bins with 40 threads:
Finished processing 0 of 20 (0.00%) bins.
Finished processing 1 of 20 (5.00%) bins.
Finished processing 2 of 20 (10.00%) bins.
Finished processing 3 of 20 (15.00%) bins.
Finished processing 4 of 20 (20.00%) bins.
Finished processing 5 of 20 (25.00%) bins.
Finished processing 6 of 20 (30.00%) bins.
Finished processing 7 of 20 (35.00%) bins.
Finished processing 8 of 20 (40.00%) bins.
Finished processing 9 of 20 (45.00%) bins.
Finished processing 10 of 20 (50.00%) bins.
Finished processing 11 of 20 (55.00%) bins.
Finished processing 12 of 20 (60.00%) bins.
Finished processing 13 of 20 (65.00%) bins.
Finished processing 14 of 20 (70.00%) bins.
Finished processing 15 of 20 (75.00%) bins.
Finished processing 16 of 20 (80.00%) bins.
Finished processing 17 of 20 (85.00%) bins.
Finished processing 18 of 20 (90.00%) bins.
Finished processing 19 of 20 (95.00%) bins.
Finished processing 20 of 20 (100.00%) bins.
Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 20 (5.00%) bins.
Finished parsing hits for 2 of 20 (10.00%) bins.
Finished parsing hits for 3 of 20 (15.00%) bins.
Finished parsing hits for 4 of 20 (20.00%) bins.
Finished parsing hits for 5 of 20 (25.00%) bins.
Finished parsing hits for 6 of 20 (30.00%) bins.
Finished parsing hits for 7 of 20 (35.00%) bins.
Finished parsing hits for 8 of 20 (40.00%) bins.
Finished parsing hits for 9 of 20 (45.00%) bins.
Finished parsing hits for 10 of 20 (50.00%) bins.
Finished parsing hits for 11 of 20 (55.00%) bins.
Finished parsing hits for 12 of 20 (60.00%) bins.
Finished parsing hits for 13 of 20 (65.00%) bins.
Finished parsing hits for 14 of 20 (70.00%) bins.
Finished parsing hits for 15 of 20 (75.00%) bins.
Finished parsing hits for 16 of 20 (80.00%) bins.
Finished parsing hits for 17 of 20 (85.00%) bins.
Finished parsing hits for 18 of 20 (90.00%) bins.
Finished parsing hits for 19 of 20 (95.00%) bins.
Finished parsing hits for 20 of 20 (100.00%) bins.
Extracting 43 HMMs with 40 threads:
Finished extracting 0 of 43 (0.00%) HMMs.
Finished extracting 1 of 43 (2.33%) HMMs.
Finished extracting 2 of 43 (4.65%) HMMs.
Finished extracting 3 of 43 (6.98%) HMMs.
Finished extracting 4 of 43 (9.30%) HMMs.
Finished extracting 5 of 43 (11.63%) HMMs.
Finished extracting 6 of 43 (13.95%) HMMs.
Finished extracting 7 of 43 (16.28%) HMMs.
Finished extracting 8 of 43 (18.60%) HMMs.
Finished extracting 9 of 43 (20.93%) HMMs.
Finished extracting 10 of 43 (23.26%) HMMs.
Finished extracting 11 of 43 (25.58%) HMMs.
Finished extracting 12 of 43 (27.91%) HMMs.
Finished extracting 13 of 43 (30.23%) HMMs.
Finished extracting 14 of 43 (32.56%) HMMs.
Finished extracting 15 of 43 (34.88%) HMMs.
Finished extracting 16 of 43 (37.21%) HMMs.
Finished extracting 17 of 43 (39.53%) HMMs.
Finished extracting 18 of 43 (41.86%) HMMs.
Finished extracting 19 of 43 (44.19%) HMMs.
Finished extracting 20 of 43 (46.51%) HMMs.
Finished extracting 21 of 43 (48.84%) HMMs.
Finished extracting 22 of 43 (51.16%) HMMs.
Finished extracting 23 of 43 (53.49%) HMMs.
Finished extracting 24 of 43 (55.81%) HMMs.
Finished extracting 25 of 43 (58.14%) HMMs.
Finished extracting 26 of 43 (60.47%) HMMs.
Finished extracting 27 of 43 (62.79%) HMMs.
Finished extracting 28 of 43 (65.12%) HMMs.
Finished extracting 29 of 43 (67.44%) HMMs.
Finished extracting 30 of 43 (69.77%) HMMs.
Finished extracting 31 of 43 (72.09%) HMMs.
Finished extracting 32 of 43 (74.42%) HMMs.
Finished extracting 33 of 43 (76.74%) HMMs.
Finished extracting 34 of 43 (79.07%) HMMs.
Finished extracting 35 of 43 (81.40%) HMMs.
Finished extracting 36 of 43 (83.72%) HMMs.
Finished extracting 37 of 43 (86.05%) HMMs.
Finished extracting 38 of 43 (88.37%) HMMs.
Finished extracting 39 of 43 (90.70%) HMMs.
Finished extracting 40 of 43 (93.02%) HMMs.
Finished extracting 41 of 43 (95.35%) HMMs.
Finished extracting 42 of 43 (97.67%) HMMs.
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 40 threads:
Finished aligning 0 of 43 (0.00%) marker genes.
Finished aligning 1 of 43 (2.33%) marker genes.
Finished aligning 2 of 43 (4.65%) marker genes.
Finished aligning 3 of 43 (6.98%) marker genes.
Finished aligning 4 of 43 (9.30%) marker genes.
Finished aligning 5 of 43 (11.63%) marker genes.
Finished aligning 6 of 43 (13.95%) marker genes.
Finished aligning 7 of 43 (16.28%) marker genes.
Finished aligning 8 of 43 (18.60%) marker genes.
Finished aligning 9 of 43 (20.93%) marker genes.
Finished aligning 10 of 43 (23.26%) marker genes.
Finished aligning 11 of 43 (25.58%) marker genes.
Finished aligning 12 of 43 (27.91%) marker genes.
Finished aligning 13 of 43 (30.23%) marker genes.
Finished aligning 14 of 43 (32.56%) marker genes.
Finished aligning 15 of 43 (34.88%) marker genes.
Finished aligning 16 of 43 (37.21%) marker genes.
Finished aligning 17 of 43 (39.53%) marker genes.
Finished aligning 18 of 43 (41.86%) marker genes.
Finished aligning 19 of 43 (44.19%) marker genes.
Finished aligning 20 of 43 (46.51%) marker genes.
Finished aligning 21 of 43 (48.84%) marker genes.
Finished aligning 22 of 43 (51.16%) marker genes.
Finished aligning 23 of 43 (53.49%) marker genes.
Finished aligning 24 of 43 (55.81%) marker genes.
Finished aligning 25 of 43 (58.14%) marker genes.
Finished aligning 26 of 43 (60.47%) marker genes.
Finished aligning 27 of 43 (62.79%) marker genes.
Finished aligning 28 of 43 (65.12%) marker genes.
Finished aligning 29 of 43 (67.44%) marker genes.
Finished aligning 30 of 43 (69.77%) marker genes.
Finished aligning 31 of 43 (72.09%) marker genes.
Finished aligning 32 of 43 (74.42%) marker genes.
Finished aligning 33 of 43 (76.74%) marker genes.
Finished aligning 34 of 43 (79.07%) marker genes.
Finished aligning 35 of 43 (81.40%) marker genes.
Finished aligning 36 of 43 (83.72%) marker genes.
Finished aligning 37 of 43 (86.05%) marker genes.
Finished aligning 38 of 43 (88.37%) marker genes.
Finished aligning 39 of 43 (90.70%) marker genes.
Finished aligning 40 of 43 (93.02%) marker genes.
Finished aligning 41 of 43 (95.35%) marker genes.
Finished aligning 42 of 43 (97.67%) marker genes.
Finished aligning 43 of 43 (100.00%) marker genes.
Reading marker alignment files.
Concatenating alignments.
Placing 20 bins into the genome tree with pplacer (be patient).
{ Current stage: 0:07:34.814 || Total: 0:07:34.814 }
*******************************************************************************
[CheckM - lineage_set] Inferring lineage-specific marker sets.
*******************************************************************************
Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 20 (5.00%) bins.
Finished parsing hits for 2 of 20 (10.00%) bins.
Finished parsing hits for 3 of 20 (15.00%) bins.
Finished parsing hits for 4 of 20 (20.00%) bins.
Finished parsing hits for 5 of 20 (25.00%) bins.
Finished parsing hits for 6 of 20 (30.00%) bins.
Finished parsing hits for 7 of 20 (35.00%) bins.
Finished parsing hits for 8 of 20 (40.00%) bins.
Finished parsing hits for 9 of 20 (45.00%) bins.
Finished parsing hits for 10 of 20 (50.00%) bins.
Finished parsing hits for 11 of 20 (55.00%) bins.
Finished parsing hits for 12 of 20 (60.00%) bins.
Finished parsing hits for 13 of 20 (65.00%) bins.
Finished parsing hits for 14 of 20 (70.00%) bins.
Finished parsing hits for 15 of 20 (75.00%) bins.
Finished parsing hits for 16 of 20 (80.00%) bins.
Finished parsing hits for 17 of 20 (85.00%) bins.
Finished parsing hits for 18 of 20 (90.00%) bins.
Finished parsing hits for 19 of 20 (95.00%) bins.
Finished parsing hits for 20 of 20 (100.00%) bins.
Determining marker sets for each genome bin.
Finished processing 1 of 20 (5.00%) bins (current: bin.1).
Finished processing 2 of 20 (10.00%) bins (current: bin.10).
Finished processing 3 of 20 (15.00%) bins (current: bin.11).
Finished processing 4 of 20 (20.00%) bins (current: bin.12).
Finished processing 5 of 20 (25.00%) bins (current: bin.13).
Finished processing 6 of 20 (30.00%) bins (current: bin.14).
Finished processing 7 of 20 (35.00%) bins (current: bin.15).
Finished processing 8 of 20 (40.00%) bins (current: bin.16).
Finished processing 9 of 20 (45.00%) bins (current: bin.17).
Finished processing 10 of 20 (50.00%) bins (current: bin.18).
Finished processing 11 of 20 (55.00%) bins (current: bin.19).
Finished processing 12 of 20 (60.00%) bins (current: bin.2).
Finished processing 13 of 20 (65.00%) bins (current: bin.3).
Finished processing 14 of 20 (70.00%) bins (current: bin.4).
Finished processing 15 of 20 (75.00%) bins (current: bin.5).
Finished processing 16 of 20 (80.00%) bins (current: bin.6).
Finished processing 17 of 20 (85.00%) bins (current: bin.7).
Finished processing 18 of 20 (90.00%) bins (current: bin.8).
Finished processing 19 of 20 (95.00%) bins (current: bin.9).
Finished processing 20 of 20 (100.00%) bins (current: bin.unbinned).
Marker set written to: INITIAL_BINNING/metabat2_bins.checkm/lineage.ms
{ Current stage: 0:00:04.415 || Total: 0:07:39.229 }
*******************************************************************************
[CheckM - analyze] Identifying marker genes in bins.
*******************************************************************************
Identifying marker genes in 20 bins with 40 threads:
Finished processing 0 of 20 (0.00%) bins.
Finished processing 1 of 20 (5.00%) bins.
Finished processing 2 of 20 (10.00%) bins.
Finished processing 3 of 20 (15.00%) bins.
Finished processing 4 of 20 (20.00%) bins.
Finished processing 5 of 20 (25.00%) bins.
Finished processing 6 of 20 (30.00%) bins.
Finished processing 7 of 20 (35.00%) bins.
Finished processing 8 of 20 (40.00%) bins.
Finished processing 9 of 20 (45.00%) bins.
Finished processing 10 of 20 (50.00%) bins.
Finished processing 11 of 20 (55.00%) bins.
Finished processing 12 of 20 (60.00%) bins.
Finished processing 13 of 20 (65.00%) bins.
Finished processing 14 of 20 (70.00%) bins.
Finished processing 15 of 20 (75.00%) bins.
Finished processing 16 of 20 (80.00%) bins.
Finished processing 17 of 20 (85.00%) bins.
Finished processing 18 of 20 (90.00%) bins.
Finished processing 19 of 20 (95.00%) bins.
Finished processing 20 of 20 (100.00%) bins.
Traceback (most recent call last):
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 274, in _run_finalizers
finalizer()
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 207, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'INITIAL_BINNING/metabat2_bins.tmp/pymp-vrQdem/.nfs000000000011959b00001e2a'
Saving HMM info to file.
{ Current stage: 0:01:36.258 || Total: 0:09:15.488 }
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 20 (5.00%) bins.
Finished parsing hits for 2 of 20 (10.00%) bins.
Finished parsing hits for 3 of 20 (15.00%) bins.
Finished parsing hits for 4 of 20 (20.00%) bins.
Finished parsing hits for 5 of 20 (25.00%) bins.
Finished parsing hits for 6 of 20 (30.00%) bins.
Finished parsing hits for 7 of 20 (35.00%) bins.
Finished parsing hits for 8 of 20 (40.00%) bins.
Finished parsing hits for 9 of 20 (45.00%) bins.
Finished parsing hits for 10 of 20 (50.00%) bins.
Finished parsing hits for 11 of 20 (55.00%) bins.
Finished parsing hits for 12 of 20 (60.00%) bins.
Finished parsing hits for 13 of 20 (65.00%) bins.
Finished parsing hits for 14 of 20 (70.00%) bins.
Finished parsing hits for 15 of 20 (75.00%) bins.
Finished parsing hits for 16 of 20 (80.00%) bins.
Finished parsing hits for 17 of 20 (85.00%) bins.
Finished parsing hits for 18 of 20 (90.00%) bins.
Finished parsing hits for 19 of 20 (95.00%) bins.
Finished parsing hits for 20 of 20 (100.00%) bins.
Aligning marker genes with multiple hits in a single bin:
Finished processing 0 of 20 (0.00%) bins.
Finished processing 1 of 20 (5.00%) bins.
Finished processing 2 of 20 (10.00%) bins.
Finished processing 3 of 20 (15.00%) bins.
Finished processing 4 of 20 (20.00%) bins.
Finished processing 5 of 20 (25.00%) bins.
Finished processing 6 of 20 (30.00%) bins.
Finished processing 7 of 20 (35.00%) bins.
Finished processing 8 of 20 (40.00%) bins.
Finished processing 9 of 20 (45.00%) bins.
Finished processing 10 of 20 (50.00%) bins.
Finished processing 11 of 20 (55.00%) bins.
Finished processing 12 of 20 (60.00%) bins.
Finished processing 13 of 20 (65.00%) bins.
Finished processing 14 of 20 (70.00%) bins.
Finished processing 15 of 20 (75.00%) bins.
Finished processing 16 of 20 (80.00%) bins.
Finished processing 17 of 20 (85.00%) bins.
Finished processing 18 of 20 (90.00%) bins.
Finished processing 19 of 20 (95.00%) bins.
Finished processing 20 of 20 (100.00%) bins.
{ Current stage: 0:00:09.768 || Total: 0:09:25.256 }
Calculating genome statistics for 20 bins with 40 threads:
Finished processing 0 of 20 (0.00%) bins.
Finished processing 1 of 20 (5.00%) bins.
Finished processing 2 of 20 (10.00%) bins.
Finished processing 3 of 20 (15.00%) bins.
Finished processing 4 of 20 (20.00%) bins.
Finished processing 5 of 20 (25.00%) bins.
Finished processing 6 of 20 (30.00%) bins.
Finished processing 7 of 20 (35.00%) bins.
Finished processing 8 of 20 (40.00%) bins.
Finished processing 9 of 20 (45.00%) bins.
Finished processing 10 of 20 (50.00%) bins.
Finished processing 11 of 20 (55.00%) bins.
Finished processing 12 of 20 (60.00%) bins.
Finished processing 13 of 20 (65.00%) bins.
Finished processing 14 of 20 (70.00%) bins.
Finished processing 15 of 20 (75.00%) bins.
Finished processing 16 of 20 (80.00%) bins.
Finished processing 17 of 20 (85.00%) bins.
Finished processing 18 of 20 (90.00%) bins.
Finished processing 19 of 20 (95.00%) bins.
Finished processing 20 of 20 (100.00%) bins.
{ Current stage: 0:00:01.180 || Total: 0:09:26.437 }
*******************************************************************************
[CheckM - qa] Tabulating genome statistics.
*******************************************************************************
Calculating AAI between multi-copy marker genes.
Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 20 (5.00%) bins.
Finished parsing hits for 2 of 20 (10.00%) bins.
Finished parsing hits for 3 of 20 (15.00%) bins.
Finished parsing hits for 4 of 20 (20.00%) bins.
Finished parsing hits for 5 of 20 (25.00%) bins.
Finished parsing hits for 6 of 20 (30.00%) bins.
Finished parsing hits for 7 of 20 (35.00%) bins.
Finished parsing hits for 8 of 20 (40.00%) bins.
Finished parsing hits for 9 of 20 (45.00%) bins.
Finished parsing hits for 10 of 20 (50.00%) bins.
Finished parsing hits for 11 of 20 (55.00%) bins.
Finished parsing hits for 12 of 20 (60.00%) bins.
Finished parsing hits for 13 of 20 (65.00%) bins.
Finished parsing hits for 14 of 20 (70.00%) bins.
Finished parsing hits for 15 of 20 (75.00%) bins.
Finished parsing hits for 16 of 20 (80.00%) bins.
Finished parsing hits for 17 of 20 (85.00%) bins.
Finished parsing hits for 18 of 20 (90.00%) bins.
Finished parsing hits for 19 of 20 (95.00%) bins.
Finished parsing hits for 20 of 20 (100.00%) bins.
{ Current stage: 0:00:07.056 || Total: 0:09:33.493 }
Output depth matrix to INITIAL_BINNING/work_files/mb2_master_depth.txt
Calculating intra contig depth variance
Output matrix to INITIAL_BINNING/work_files/mb2_master_depth.txt
Opening 3 bams
Consolidating headers
Processing bam files
Thread 2 finished: ERR011349.bam with 22886298 reads and 6744748 readsWellMapped
Thread 1 finished: ERR011348.bam with 20878028 reads and 6998908 readsWellMapped
Thread 0 finished: ERR011347.bam with 24089298 reads and 9022106 readsWellMapped
Creating depth matrix file: INITIAL_BINNING/work_files/mb2_master_depth.txt
Closing most bam files
Closing last bam file
Finished
readline() on closed filehandle FILE at /home/*********/anaconda2/envs/metawrap/bin/run_MaxBin.pl line 1336.
readline() on closed filehandle FILE at /home/*********/anaconda2/envs/metawrap/bin/run_MaxBin.pl line 1336.
*******************************************************************************
[CheckM - tree] Placing bins in reference genome tree.
*******************************************************************************
Identifying marker genes in 13 bins with 40 threads:
Finished processing 0 of 13 (0.00%) bins.
Finished processing 1 of 13 (7.69%) bins.
Finished processing 2 of 13 (15.38%) bins.
Finished processing 3 of 13 (23.08%) bins.
Finished processing 4 of 13 (30.77%) bins.
Finished processing 5 of 13 (38.46%) bins.
Finished processing 6 of 13 (46.15%) bins.
Finished processing 7 of 13 (53.85%) bins.
Finished processing 8 of 13 (61.54%) bins.
Finished processing 9 of 13 (69.23%) bins.
Finished processing 10 of 13 (76.92%) bins.
Finished processing 11 of 13 (84.62%) bins.
Finished processing 12 of 13 (92.31%) bins.
Finished processing 13 of 13 (100.00%) bins.
Traceback (most recent call last):
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 274, in _run_finalizers
finalizer()
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 207, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'INITIAL_BINNING/maxbin2_bins.tmp/pymp-IRyzVG/.nfs0000000000119aeb00001e3e'
Saving HMM info to file.
Calculating genome statistics for 13 bins with 40 threads:
Finished processing 0 of 13 (0.00%) bins.
Finished processing 1 of 13 (7.69%) bins.
Finished processing 2 of 13 (15.38%) bins.
Finished processing 3 of 13 (23.08%) bins.
Finished processing 4 of 13 (30.77%) bins.
Finished processing 5 of 13 (38.46%) bins.
Finished processing 6 of 13 (46.15%) bins.
Finished processing 7 of 13 (53.85%) bins.
Finished processing 8 of 13 (61.54%) bins.
Finished processing 9 of 13 (69.23%) bins.
Finished processing 10 of 13 (76.92%) bins.
Finished processing 11 of 13 (84.62%) bins.
Finished processing 12 of 13 (92.31%) bins.
Finished processing 13 of 13 (100.00%) bins.
Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 13 (7.69%) bins.
Finished parsing hits for 2 of 13 (15.38%) bins.
Finished parsing hits for 3 of 13 (23.08%) bins.
Finished parsing hits for 4 of 13 (30.77%) bins.
Finished parsing hits for 5 of 13 (38.46%) bins.
Finished parsing hits for 6 of 13 (46.15%) bins.
Finished parsing hits for 7 of 13 (53.85%) bins.
Finished parsing hits for 8 of 13 (61.54%) bins.
Finished parsing hits for 9 of 13 (69.23%) bins.
Finished parsing hits for 10 of 13 (76.92%) bins.
Finished parsing hits for 11 of 13 (84.62%) bins.
Finished parsing hits for 12 of 13 (92.31%) bins.
Finished parsing hits for 13 of 13 (100.00%) bins.
Extracting 43 HMMs with 40 threads:
Finished extracting 0 of 43 (0.00%) HMMs.
Finished extracting 1 of 43 (2.33%) HMMs.
Finished extracting 2 of 43 (4.65%) HMMs.
Finished extracting 3 of 43 (6.98%) HMMs.
Finished extracting 4 of 43 (9.30%) HMMs.
Finished extracting 5 of 43 (11.63%) HMMs.
Finished extracting 6 of 43 (13.95%) HMMs.
Finished extracting 7 of 43 (16.28%) HMMs.
Finished extracting 8 of 43 (18.60%) HMMs.
Finished extracting 9 of 43 (20.93%) HMMs.
Finished extracting 10 of 43 (23.26%) HMMs.
Finished extracting 11 of 43 (25.58%) HMMs.
Finished extracting 12 of 43 (27.91%) HMMs.
Finished extracting 13 of 43 (30.23%) HMMs.
Finished extracting 14 of 43 (32.56%) HMMs.
Finished extracting 15 of 43 (34.88%) HMMs.
Finished extracting 16 of 43 (37.21%) HMMs.
Finished extracting 17 of 43 (39.53%) HMMs.
Finished extracting 18 of 43 (41.86%) HMMs.
Finished extracting 19 of 43 (44.19%) HMMs.
Finished extracting 20 of 43 (46.51%) HMMs.
Finished extracting 21 of 43 (48.84%) HMMs.
Finished extracting 22 of 43 (51.16%) HMMs.
Finished extracting 23 of 43 (53.49%) HMMs.
Finished extracting 24 of 43 (55.81%) HMMs.
Finished extracting 25 of 43 (58.14%) HMMs.
Finished extracting 26 of 43 (60.47%) HMMs.
Finished extracting 27 of 43 (62.79%) HMMs.
Finished extracting 28 of 43 (65.12%) HMMs.
Finished extracting 29 of 43 (67.44%) HMMs.
Finished extracting 30 of 43 (69.77%) HMMs.
Finished extracting 31 of 43 (72.09%) HMMs.
Finished extracting 32 of 43 (74.42%) HMMs.
Finished extracting 33 of 43 (76.74%) HMMs.
Finished extracting 34 of 43 (79.07%) HMMs.
Finished extracting 35 of 43 (81.40%) HMMs.
Finished extracting 36 of 43 (83.72%) HMMs.
Finished extracting 37 of 43 (86.05%) HMMs.
Finished extracting 38 of 43 (88.37%) HMMs.
Finished extracting 39 of 43 (90.70%) HMMs.
Finished extracting 40 of 43 (93.02%) HMMs.
Finished extracting 41 of 43 (95.35%) HMMs.
Finished extracting 42 of 43 (97.67%) HMMs.
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 40 threads:
Finished aligning 0 of 43 (0.00%) marker genes.
Finished aligning 1 of 43 (2.33%) marker genes.
Finished aligning 2 of 43 (4.65%) marker genes.
Finished aligning 3 of 43 (6.98%) marker genes.
Finished aligning 4 of 43 (9.30%) marker genes.
Finished aligning 5 of 43 (11.63%) marker genes.
Finished aligning 6 of 43 (13.95%) marker genes.
Finished aligning 7 of 43 (16.28%) marker genes.
Finished aligning 8 of 43 (18.60%) marker genes.
Finished aligning 9 of 43 (20.93%) marker genes.
Finished aligning 10 of 43 (23.26%) marker genes.
Finished aligning 11 of 43 (25.58%) marker genes.
Finished aligning 12 of 43 (27.91%) marker genes.
Finished aligning 13 of 43 (30.23%) marker genes.
Finished aligning 14 of 43 (32.56%) marker genes.
Finished aligning 15 of 43 (34.88%) marker genes.
Finished aligning 16 of 43 (37.21%) marker genes.
Finished aligning 17 of 43 (39.53%) marker genes.
Finished aligning 18 of 43 (41.86%) marker genes.
Finished aligning 19 of 43 (44.19%) marker genes.
Finished aligning 20 of 43 (46.51%) marker genes.
Finished aligning 21 of 43 (48.84%) marker genes.
Finished aligning 22 of 43 (51.16%) marker genes.
Finished aligning 23 of 43 (53.49%) marker genes.
Finished aligning 24 of 43 (55.81%) marker genes.
Finished aligning 25 of 43 (58.14%) marker genes.
Finished aligning 26 of 43 (60.47%) marker genes.
Finished aligning 27 of 43 (62.79%) marker genes.
Finished aligning 28 of 43 (65.12%) marker genes.
Finished aligning 29 of 43 (67.44%) marker genes.
Finished aligning 30 of 43 (69.77%) marker genes.
Finished aligning 31 of 43 (72.09%) marker genes.
Finished aligning 32 of 43 (74.42%) marker genes.
Finished aligning 33 of 43 (76.74%) marker genes.
Finished aligning 34 of 43 (79.07%) marker genes.
Finished aligning 35 of 43 (81.40%) marker genes.
Finished aligning 36 of 43 (83.72%) marker genes.
Finished aligning 37 of 43 (86.05%) marker genes.
Finished aligning 38 of 43 (88.37%) marker genes.
Finished aligning 39 of 43 (90.70%) marker genes.
Finished aligning 40 of 43 (93.02%) marker genes.
Finished aligning 41 of 43 (95.35%) marker genes.
Finished aligning 42 of 43 (97.67%) marker genes.
Finished aligning 43 of 43 (100.00%) marker genes.
Reading marker alignment files.
Concatenating alignments.
Placing 13 bins into the genome tree with pplacer (be patient).
{ Current stage: 0:07:34.228 || Total: 0:07:34.228 }
*******************************************************************************
[CheckM - lineage_set] Inferring lineage-specific marker sets.
*******************************************************************************
Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 13 (7.69%) bins.
Finished parsing hits for 2 of 13 (15.38%) bins.
Finished parsing hits for 3 of 13 (23.08%) bins.
Finished parsing hits for 4 of 13 (30.77%) bins.
Finished parsing hits for 5 of 13 (38.46%) bins.
Finished parsing hits for 6 of 13 (46.15%) bins.
Finished parsing hits for 7 of 13 (53.85%) bins.
Finished parsing hits for 8 of 13 (61.54%) bins.
Finished parsing hits for 9 of 13 (69.23%) bins.
Finished parsing hits for 10 of 13 (76.92%) bins.
Finished parsing hits for 11 of 13 (84.62%) bins.
Finished parsing hits for 12 of 13 (92.31%) bins.
Finished parsing hits for 13 of 13 (100.00%) bins.
Determining marker sets for each genome bin.
Finished processing 1 of 13 (7.69%) bins (current: bin.0).
Finished processing 2 of 13 (15.38%) bins (current: bin.1).
Finished processing 3 of 13 (23.08%) bins (current: bin.10).
Finished processing 4 of 13 (30.77%) bins (current: bin.11).
Finished processing 5 of 13 (38.46%) bins (current: bin.12).
Finished processing 6 of 13 (46.15%) bins (current: bin.2).
Finished processing 7 of 13 (53.85%) bins (current: bin.3).
Finished processing 8 of 13 (61.54%) bins (current: bin.4).
Finished processing 9 of 13 (69.23%) bins (current: bin.5).
Finished processing 10 of 13 (76.92%) bins (current: bin.6).
Finished processing 11 of 13 (84.62%) bins (current: bin.7).
Finished processing 12 of 13 (92.31%) bins (current: bin.8).
Finished processing 13 of 13 (100.00%) bins (current: bin.9).
Marker set written to: INITIAL_BINNING/maxbin2_bins.checkm/lineage.ms
{ Current stage: 0:00:03.560 || Total: 0:07:37.789 }
*******************************************************************************
[CheckM - analyze] Identifying marker genes in bins.
*******************************************************************************
Identifying marker genes in 13 bins with 40 threads:
Finished processing 0 of 13 (0.00%) bins.
Finished processing 1 of 13 (7.69%) bins.
Finished processing 2 of 13 (15.38%) bins.
Finished processing 3 of 13 (23.08%) bins.
Finished processing 4 of 13 (30.77%) bins.
Finished processing 5 of 13 (38.46%) bins.
Finished processing 6 of 13 (46.15%) bins.
Finished processing 7 of 13 (53.85%) bins.
Finished processing 8 of 13 (61.54%) bins.
Finished processing 9 of 13 (69.23%) bins.
Finished processing 10 of 13 (76.92%) bins.
Finished processing 11 of 13 (84.62%) bins.
Finished processing 12 of 13 (92.31%) bins.
Finished processing 13 of 13 (100.00%) bins.
Traceback (most recent call last):
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 274, in _run_finalizers
finalizer()
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 207, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'INITIAL_BINNING/maxbin2_bins.tmp/pymp-Ibactk/.nfs0000000000119b6e00001e4c'
Saving HMM info to file.
{ Current stage: 0:01:27.619 || Total: 0:09:05.408 }
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 13 (7.69%) bins.
Finished parsing hits for 2 of 13 (15.38%) bins.
Finished parsing hits for 3 of 13 (23.08%) bins.
Finished parsing hits for 4 of 13 (30.77%) bins.
Finished parsing hits for 5 of 13 (38.46%) bins.
Finished parsing hits for 6 of 13 (46.15%) bins.
Finished parsing hits for 7 of 13 (53.85%) bins.
Finished parsing hits for 8 of 13 (61.54%) bins.
Finished parsing hits for 9 of 13 (69.23%) bins.
Finished parsing hits for 10 of 13 (76.92%) bins.
Finished parsing hits for 11 of 13 (84.62%) bins.
Finished parsing hits for 12 of 13 (92.31%) bins.
Finished parsing hits for 13 of 13 (100.00%) bins.
Aligning marker genes with multiple hits in a single bin:
Finished processing 0 of 13 (0.00%) bins.
Finished processing 1 of 13 (7.69%) bins.
Finished processing 2 of 13 (15.38%) bins.
Finished processing 3 of 13 (23.08%) bins.
Finished processing 4 of 13 (30.77%) bins.
Finished processing 5 of 13 (38.46%) bins.
Finished processing 6 of 13 (46.15%) bins.
Finished processing 7 of 13 (53.85%) bins.
Finished processing 8 of 13 (61.54%) bins.
Finished processing 9 of 13 (69.23%) bins.
Finished processing 10 of 13 (76.92%) bins.
Finished processing 11 of 13 (84.62%) bins.
Finished processing 12 of 13 (92.31%) bins.
Finished processing 13 of 13 (100.00%) bins.
{ Current stage: 0:00:08.774 || Total: 0:09:14.183 }
Calculating genome statistics for 13 bins with 40 threads:
Finished processing 0 of 13 (0.00%) bins.
Finished processing 1 of 13 (7.69%) bins.
Finished processing 2 of 13 (15.38%) bins.
Finished processing 3 of 13 (23.08%) bins.
Finished processing 4 of 13 (30.77%) bins.
Finished processing 5 of 13 (38.46%) bins.
Finished processing 6 of 13 (46.15%) bins.
Finished processing 7 of 13 (53.85%) bins.
Finished processing 8 of 13 (61.54%) bins.
Finished processing 9 of 13 (69.23%) bins.
Finished processing 10 of 13 (76.92%) bins.
Finished processing 11 of 13 (84.62%) bins.
Finished processing 12 of 13 (92.31%) bins.
Finished processing 13 of 13 (100.00%) bins.
{ Current stage: 0:00:00.459 || Total: 0:09:14.642 }
*******************************************************************************
[CheckM - qa] Tabulating genome statistics.
*******************************************************************************
Calculating AAI between multi-copy marker genes.
Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 13 (7.69%) bins.
Finished parsing hits for 2 of 13 (15.38%) bins.
Finished parsing hits for 3 of 13 (23.08%) bins.
Finished parsing hits for 4 of 13 (30.77%) bins.
Finished parsing hits for 5 of 13 (38.46%) bins.
Finished parsing hits for 6 of 13 (46.15%) bins.
Finished parsing hits for 7 of 13 (53.85%) bins.
Finished parsing hits for 8 of 13 (61.54%) bins.
Finished parsing hits for 9 of 13 (69.23%) bins.
Finished parsing hits for 10 of 13 (76.92%) bins.
Finished parsing hits for 11 of 13 (84.62%) bins.
Finished parsing hits for 12 of 13 (92.31%) bins.
Finished parsing hits for 13 of 13 (100.00%) bins.
{ Current stage: 0:00:06.590 || Total: 0:09:21.232 }
Output depth matrix to INITIAL_BINNING/work_files/tmp
Calculating intra contig depth variance
Output matrix to INITIAL_BINNING/work_files/tmp
Opening 3 bams
Consolidating headers
Processing bam files
Thread 2 finished: ERR011349.bam with 22886298 reads and 6744748 readsWellMapped
Thread 1 finished: ERR011348.bam with 20878028 reads and 6998908 readsWellMapped
Thread 0 finished: ERR011347.bam with 24089298 reads and 9022106 readsWellMapped
Creating depth matrix file: INITIAL_BINNING/work_files/tmp
Closing most bam files
Closing last bam file
Finished
Up and running. Check /home/*********/Work_space/metawrap_sample/INITIAL_BINNING/work_files/concoct_out/log.txt for progress
/home/*********/anaconda2/envs/metawrap/lib/python2.7/site-packages/Bio/Seq.py:345: BiopythonDeprecationWarning: This method is obsolete; please use str(my_seq) instead of my_seq.tostring().
BiopythonDeprecationWarning)
CONCOCT Finished, the log shows how it went.
*******************************************************************************
[CheckM - tree] Placing bins in reference genome tree.
*******************************************************************************
Identifying marker genes in 38 bins with 40 threads:
Finished processing 0 of 38 (0.00%) bins.
Finished processing 1 of 38 (2.63%) bins.
Finished processing 2 of 38 (5.26%) bins.
Finished processing 3 of 38 (7.89%) bins.
Finished processing 4 of 38 (10.53%) bins.
Finished processing 5 of 38 (13.16%) bins.
Finished processing 6 of 38 (15.79%) bins.
Finished processing 7 of 38 (18.42%) bins.
Finished processing 8 of 38 (21.05%) bins.
Finished processing 9 of 38 (23.68%) bins.
Finished processing 10 of 38 (26.32%) bins.
Finished processing 11 of 38 (28.95%) bins.
Finished processing 12 of 38 (31.58%) bins.
Finished processing 13 of 38 (34.21%) bins.
Finished processing 14 of 38 (36.84%) bins.
Finished processing 15 of 38 (39.47%) bins.
Finished processing 16 of 38 (42.11%) bins.
Finished processing 17 of 38 (44.74%) bins.
Finished processing 18 of 38 (47.37%) bins.
Finished processing 19 of 38 (50.00%) bins.
Finished processing 20 of 38 (52.63%) bins.
Finished processing 21 of 38 (55.26%) bins.
Finished processing 22 of 38 (57.89%) bins.
Finished processing 23 of 38 (60.53%) bins.
Finished processing 24 of 38 (63.16%) bins.
Finished processing 25 of 38 (65.79%) bins.
Finished processing 26 of 38 (68.42%) bins.
Finished processing 27 of 38 (71.05%) bins.
Finished processing 28 of 38 (73.68%) bins.
Finished processing 29 of 38 (76.32%) bins.
Finished processing 30 of 38 (78.95%) bins.
Finished processing 31 of 38 (81.58%) bins.
Finished processing 32 of 38 (84.21%) bins.
Finished processing 33 of 38 (86.84%) bins.
Finished processing 34 of 38 (89.47%) bins.
Finished processing 35 of 38 (92.11%) bins.
Finished processing 36 of 38 (94.74%) bins.
Finished processing 37 of 38 (97.37%) bins.
Finished processing 38 of 38 (100.00%) bins.
Traceback (most recent call last):
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 274, in _run_finalizers
finalizer()
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 207, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'INITIAL_BINNING/concoct_bins.tmp/pymp-9vh3P1/.nfs000000000011df6800001e77'
Saving HMM info to file.
Calculating genome statistics for 38 bins with 40 threads:
Finished processing 0 of 38 (0.00%) bins.
Finished processing 1 of 38 (2.63%) bins.
Finished processing 2 of 38 (5.26%) bins.
Finished processing 3 of 38 (7.89%) bins.
Finished processing 4 of 38 (10.53%) bins.
Finished processing 5 of 38 (13.16%) bins.
Finished processing 6 of 38 (15.79%) bins.
Finished processing 7 of 38 (18.42%) bins.
Finished processing 8 of 38 (21.05%) bins.
Finished processing 9 of 38 (23.68%) bins.
Finished processing 10 of 38 (26.32%) bins.
Finished processing 11 of 38 (28.95%) bins.
Finished processing 12 of 38 (31.58%) bins.
Finished processing 13 of 38 (34.21%) bins.
Finished processing 14 of 38 (36.84%) bins.
Finished processing 15 of 38 (39.47%) bins.
Finished processing 16 of 38 (42.11%) bins.
Finished processing 17 of 38 (44.74%) bins.
Finished processing 18 of 38 (47.37%) bins.
Finished processing 19 of 38 (50.00%) bins.
Finished processing 20 of 38 (52.63%) bins.
Finished processing 21 of 38 (55.26%) bins.
Finished processing 22 of 38 (57.89%) bins.
Finished processing 23 of 38 (60.53%) bins.
Finished processing 24 of 38 (63.16%) bins.
Finished processing 25 of 38 (65.79%) bins.
Finished processing 26 of 38 (68.42%) bins.
Finished processing 27 of 38 (71.05%) bins.
Finished processing 28 of 38 (73.68%) bins.
Finished processing 29 of 38 (76.32%) bins.
Finished processing 30 of 38 (78.95%) bins.
Finished processing 31 of 38 (81.58%) bins.
Finished processing 32 of 38 (84.21%) bins.
Finished processing 33 of 38 (86.84%) bins.
Finished processing 34 of 38 (89.47%) bins.
Finished processing 35 of 38 (92.11%) bins.
Finished processing 36 of 38 (94.74%) bins.
Finished processing 37 of 38 (97.37%) bins.
Finished processing 38 of 38 (100.00%) bins.
Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 38 (2.63%) bins.
Finished parsing hits for 2 of 38 (5.26%) bins.
Finished parsing hits for 3 of 38 (7.89%) bins.
Finished parsing hits for 4 of 38 (10.53%) bins.
Finished parsing hits for 5 of 38 (13.16%) bins.
Finished parsing hits for 6 of 38 (15.79%) bins.
Finished parsing hits for 7 of 38 (18.42%) bins.
Finished parsing hits for 8 of 38 (21.05%) bins.
Finished parsing hits for 9 of 38 (23.68%) bins.
Finished parsing hits for 10 of 38 (26.32%) bins.
Finished parsing hits for 11 of 38 (28.95%) bins.
Finished parsing hits for 12 of 38 (31.58%) bins.
Finished parsing hits for 13 of 38 (34.21%) bins.
Finished parsing hits for 14 of 38 (36.84%) bins.
Finished parsing hits for 15 of 38 (39.47%) bins.
Finished parsing hits for 16 of 38 (42.11%) bins.
Finished parsing hits for 17 of 38 (44.74%) bins.
Finished parsing hits for 18 of 38 (47.37%) bins.
Finished parsing hits for 19 of 38 (50.00%) bins.
Finished parsing hits for 20 of 38 (52.63%) bins.
Finished parsing hits for 21 of 38 (55.26%) bins.
Finished parsing hits for 22 of 38 (57.89%) bins.
Finished parsing hits for 23 of 38 (60.53%) bins.
Finished parsing hits for 24 of 38 (63.16%) bins.
Finished parsing hits for 25 of 38 (65.79%) bins.
Finished parsing hits for 26 of 38 (68.42%) bins.
Finished parsing hits for 27 of 38 (71.05%) bins.
Finished parsing hits for 28 of 38 (73.68%) bins.
Finished parsing hits for 29 of 38 (76.32%) bins.
Finished parsing hits for 30 of 38 (78.95%) bins.
Finished parsing hits for 31 of 38 (81.58%) bins.
Finished parsing hits for 32 of 38 (84.21%) bins.
Finished parsing hits for 33 of 38 (86.84%) bins.
Finished parsing hits for 34 of 38 (89.47%) bins.
Finished parsing hits for 35 of 38 (92.11%) bins.
Finished parsing hits for 36 of 38 (94.74%) bins.
Finished parsing hits for 37 of 38 (97.37%) bins.
Finished parsing hits for 38 of 38 (100.00%) bins.
Extracting 43 HMMs with 40 threads:
Finished extracting 0 of 43 (0.00%) HMMs.
Finished extracting 1 of 43 (2.33%) HMMs.
Finished extracting 2 of 43 (4.65%) HMMs.
Finished extracting 3 of 43 (6.98%) HMMs.
Finished extracting 4 of 43 (9.30%) HMMs.
Finished extracting 5 of 43 (11.63%) HMMs.
Finished extracting 6 of 43 (13.95%) HMMs.
Finished extracting 7 of 43 (16.28%) HMMs.
Finished extracting 8 of 43 (18.60%) HMMs.
Finished extracting 9 of 43 (20.93%) HMMs.
Finished extracting 10 of 43 (23.26%) HMMs.
Finished extracting 11 of 43 (25.58%) HMMs.
Finished extracting 12 of 43 (27.91%) HMMs.
Finished extracting 13 of 43 (30.23%) HMMs.
Finished extracting 14 of 43 (32.56%) HMMs.
Finished extracting 15 of 43 (34.88%) HMMs.
Finished extracting 16 of 43 (37.21%) HMMs.
Finished extracting 17 of 43 (39.53%) HMMs.
Finished extracting 18 of 43 (41.86%) HMMs.
Finished extracting 19 of 43 (44.19%) HMMs.
Finished extracting 20 of 43 (46.51%) HMMs.
Finished extracting 21 of 43 (48.84%) HMMs.
Finished extracting 22 of 43 (51.16%) HMMs.
Finished extracting 23 of 43 (53.49%) HMMs.
Finished extracting 24 of 43 (55.81%) HMMs.
Finished extracting 25 of 43 (58.14%) HMMs.
Finished extracting 26 of 43 (60.47%) HMMs.
Finished extracting 27 of 43 (62.79%) HMMs.
Finished extracting 28 of 43 (65.12%) HMMs.
Finished extracting 29 of 43 (67.44%) HMMs.
Finished extracting 30 of 43 (69.77%) HMMs.
Finished extracting 31 of 43 (72.09%) HMMs.
Finished extracting 32 of 43 (74.42%) HMMs.
Finished extracting 33 of 43 (76.74%) HMMs.
Finished extracting 34 of 43 (79.07%) HMMs.
Finished extracting 35 of 43 (81.40%) HMMs.
Finished extracting 36 of 43 (83.72%) HMMs.
Finished extracting 37 of 43 (86.05%) HMMs.
Finished extracting 38 of 43 (88.37%) HMMs.
Finished extracting 39 of 43 (90.70%) HMMs.
Finished extracting 40 of 43 (93.02%) HMMs.
Finished extracting 41 of 43 (95.35%) HMMs.
Finished extracting 42 of 43 (97.67%) HMMs.
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 40 threads:
Finished aligning 0 of 43 (0.00%) marker genes.
Finished aligning 1 of 43 (2.33%) marker genes.
Finished aligning 2 of 43 (4.65%) marker genes.
Finished aligning 3 of 43 (6.98%) marker genes.
Finished aligning 4 of 43 (9.30%) marker genes.
Finished aligning 5 of 43 (11.63%) marker genes.
Finished aligning 6 of 43 (13.95%) marker genes.
Finished aligning 7 of 43 (16.28%) marker genes.
Finished aligning 8 of 43 (18.60%) marker genes.
Finished aligning 9 of 43 (20.93%) marker genes.
Finished aligning 10 of 43 (23.26%) marker genes.
Finished aligning 11 of 43 (25.58%) marker genes.
Finished aligning 12 of 43 (27.91%) marker genes.
Finished aligning 13 of 43 (30.23%) marker genes.
Finished aligning 14 of 43 (32.56%) marker genes.
Finished aligning 15 of 43 (34.88%) marker genes.
Finished aligning 16 of 43 (37.21%) marker genes.
Finished aligning 17 of 43 (39.53%) marker genes.
Finished aligning 18 of 43 (41.86%) marker genes.
Finished aligning 19 of 43 (44.19%) marker genes.
Finished aligning 20 of 43 (46.51%) marker genes.
Finished aligning 21 of 43 (48.84%) marker genes.
Finished aligning 22 of 43 (51.16%) marker genes.
Finished aligning 23 of 43 (53.49%) marker genes.
Finished aligning 24 of 43 (55.81%) marker genes.
Finished aligning 25 of 43 (58.14%) marker genes.
Finished aligning 26 of 43 (60.47%) marker genes.
Finished aligning 27 of 43 (62.79%) marker genes.
Finished aligning 28 of 43 (65.12%) marker genes.
Finished aligning 29 of 43 (67.44%) marker genes.
Finished aligning 30 of 43 (69.77%) marker genes.
Finished aligning 31 of 43 (72.09%) marker genes.
Finished aligning 32 of 43 (74.42%) marker genes.
Finished aligning 33 of 43 (76.74%) marker genes.
Finished aligning 34 of 43 (79.07%) marker genes.
Finished aligning 35 of 43 (81.40%) marker genes.
Finished aligning 36 of 43 (83.72%) marker genes.
Finished aligning 37 of 43 (86.05%) marker genes.
Finished aligning 38 of 43 (88.37%) marker genes.
Finished aligning 39 of 43 (90.70%) marker genes.
Finished aligning 40 of 43 (93.02%) marker genes.
Finished aligning 41 of 43 (95.35%) marker genes.
Finished aligning 42 of 43 (97.67%) marker genes.
Finished aligning 43 of 43 (100.00%) marker genes.
Reading marker alignment files.
Concatenating alignments.
Placing 38 bins into the genome tree with pplacer (be patient).
{ Current stage: 0:08:18.433 || Total: 0:08:18.433 }
*******************************************************************************
[CheckM - lineage_set] Inferring lineage-specific marker sets.
*******************************************************************************
Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 38 (2.63%) bins.
Finished parsing hits for 2 of 38 (5.26%) bins.
Finished parsing hits for 3 of 38 (7.89%) bins.
Finished parsing hits for 4 of 38 (10.53%) bins.
Finished parsing hits for 5 of 38 (13.16%) bins.
Finished parsing hits for 6 of 38 (15.79%) bins.
Finished parsing hits for 7 of 38 (18.42%) bins.
Finished parsing hits for 8 of 38 (21.05%) bins.
Finished parsing hits for 9 of 38 (23.68%) bins.
Finished parsing hits for 10 of 38 (26.32%) bins.
Finished parsing hits for 11 of 38 (28.95%) bins.
Finished parsing hits for 12 of 38 (31.58%) bins.
Finished parsing hits for 13 of 38 (34.21%) bins.
Finished parsing hits for 14 of 38 (36.84%) bins.
Finished parsing hits for 15 of 38 (39.47%) bins.
Finished parsing hits for 16 of 38 (42.11%) bins.
Finished parsing hits for 17 of 38 (44.74%) bins.
Finished parsing hits for 18 of 38 (47.37%) bins.
Finished parsing hits for 19 of 38 (50.00%) bins.
Finished parsing hits for 20 of 38 (52.63%) bins.
Finished parsing hits for 21 of 38 (55.26%) bins.
Finished parsing hits for 22 of 38 (57.89%) bins.
Finished parsing hits for 23 of 38 (60.53%) bins.
Finished parsing hits for 24 of 38 (63.16%) bins.
Finished parsing hits for 25 of 38 (65.79%) bins.
Finished parsing hits for 26 of 38 (68.42%) bins.
Finished parsing hits for 27 of 38 (71.05%) bins.
Finished parsing hits for 28 of 38 (73.68%) bins.
Finished parsing hits for 29 of 38 (76.32%) bins.
Finished parsing hits for 30 of 38 (78.95%) bins.
Finished parsing hits for 31 of 38 (81.58%) bins.
Finished parsing hits for 32 of 38 (84.21%) bins.
Finished parsing hits for 33 of 38 (86.84%) bins.
Finished parsing hits for 34 of 38 (89.47%) bins.
Finished parsing hits for 35 of 38 (92.11%) bins.
Finished parsing hits for 36 of 38 (94.74%) bins.
Finished parsing hits for 37 of 38 (97.37%) bins.
Finished parsing hits for 38 of 38 (100.00%) bins.
Determining marker sets for each genome bin.
Finished processing 1 of 38 (2.63%) bins (current: bin.0).
Finished processing 2 of 38 (5.26%) bins (current: bin.1).
Finished processing 3 of 38 (7.89%) bins (current: bin.10).
Finished processing 4 of 38 (10.53%) bins (current: bin.11).
Finished processing 5 of 38 (13.16%) bins (current: bin.12).
Finished processing 6 of 38 (15.79%) bins (current: bin.13).
Finished processing 7 of 38 (18.42%) bins (current: bin.14).
Finished processing 8 of 38 (21.05%) bins (current: bin.15).
Finished processing 9 of 38 (23.68%) bins (current: bin.16).
Finished processing 10 of 38 (26.32%) bins (current: bin.17).
Finished processing 11 of 38 (28.95%) bins (current: bin.18).
Finished processing 12 of 38 (31.58%) bins (current: bin.19).
Finished processing 13 of 38 (34.21%) bins (current: bin.2).
Finished processing 14 of 38 (36.84%) bins (current: bin.20).
Finished processing 15 of 38 (39.47%) bins (current: bin.21).
Finished processing 16 of 38 (42.11%) bins (current: bin.22).
Finished processing 17 of 38 (44.74%) bins (current: bin.23).
Finished processing 18 of 38 (47.37%) bins (current: bin.24).
Finished processing 19 of 38 (50.00%) bins (current: bin.25).
Finished processing 20 of 38 (52.63%) bins (current: bin.26).
Finished processing 21 of 38 (55.26%) bins (current: bin.27).
Finished processing 22 of 38 (57.89%) bins (current: bin.28).
Finished processing 23 of 38 (60.53%) bins (current: bin.29).
Finished processing 24 of 38 (63.16%) bins (current: bin.3).
Finished processing 25 of 38 (65.79%) bins (current: bin.30).
Finished processing 26 of 38 (68.42%) bins (current: bin.31).
Finished processing 27 of 38 (71.05%) bins (current: bin.32).
Finished processing 28 of 38 (73.68%) bins (current: bin.33).
Finished processing 29 of 38 (76.32%) bins (current: bin.34).
Finished processing 30 of 38 (78.95%) bins (current: bin.35).
Finished processing 31 of 38 (81.58%) bins (current: bin.36).
Finished processing 32 of 38 (84.21%) bins (current: bin.4).
Finished processing 33 of 38 (86.84%) bins (current: bin.5).
Finished processing 34 of 38 (89.47%) bins (current: bin.6).
Finished processing 35 of 38 (92.11%) bins (current: bin.7).
Finished processing 36 of 38 (94.74%) bins (current: bin.8).
Finished processing 37 of 38 (97.37%) bins (current: bin.9).
Finished processing 38 of 38 (100.00%) bins (current: unbinned).
Marker set written to: INITIAL_BINNING/concoct_bins.checkm/lineage.ms
{ Current stage: 0:00:06.938 || Total: 0:08:25.372 }
*******************************************************************************
[CheckM - analyze] Identifying marker genes in bins.
*******************************************************************************
Identifying marker genes in 38 bins with 40 threads:
Finished processing 0 of 38 (0.00%) bins.
Finished processing 1 of 38 (2.63%) bins.
Finished processing 2 of 38 (5.26%) bins.
Finished processing 3 of 38 (7.89%) bins.
Finished processing 4 of 38 (10.53%) bins.
Finished processing 5 of 38 (13.16%) bins.
Finished processing 6 of 38 (15.79%) bins.
Finished processing 7 of 38 (18.42%) bins.
Finished processing 8 of 38 (21.05%) bins.
Finished processing 9 of 38 (23.68%) bins.
Finished processing 10 of 38 (26.32%) bins.
Finished processing 11 of 38 (28.95%) bins.
Finished processing 12 of 38 (31.58%) bins.
Finished processing 13 of 38 (34.21%) bins.
Finished processing 14 of 38 (36.84%) bins.
Finished processing 15 of 38 (39.47%) bins.
Finished processing 16 of 38 (42.11%) bins.
Finished processing 17 of 38 (44.74%) bins.
Finished processing 18 of 38 (47.37%) bins.
Finished processing 19 of 38 (50.00%) bins.
Finished processing 20 of 38 (52.63%) bins.
Finished processing 21 of 38 (55.26%) bins.
Finished processing 22 of 38 (57.89%) bins.
Finished processing 23 of 38 (60.53%) bins.
Finished processing 24 of 38 (63.16%) bins.
Finished processing 25 of 38 (65.79%) bins.
Finished processing 26 of 38 (68.42%) bins.
Finished processing 27 of 38 (71.05%) bins.
Finished processing 28 of 38 (73.68%) bins.
Finished processing 29 of 38 (76.32%) bins.
Finished processing 30 of 38 (78.95%) bins.
Finished processing 31 of 38 (81.58%) bins.
Finished processing 32 of 38 (84.21%) bins.
Finished processing 33 of 38 (86.84%) bins.
Finished processing 34 of 38 (89.47%) bins.
Finished processing 35 of 38 (92.11%) bins.
Finished processing 36 of 38 (94.74%) bins.
Finished processing 37 of 38 (97.37%) bins.
Finished processing 38 of 38 (100.00%) bins.
Traceback (most recent call last):
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 274, in _run_finalizers
finalizer()
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/multiprocessing/util.py", line 207, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/home/*********/anaconda2/envs/metawrap/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'INITIAL_BINNING/concoct_bins.tmp/pymp-aq76b9/.nfs0000000000119cfc00001e9e'
Saving HMM info to file.
{ Current stage: 0:02:00.745 || Total: 0:10:26.117 }
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 38 (2.63%) bins.
Finished parsing hits for 2 of 38 (5.26%) bins.
Finished parsing hits for 3 of 38 (7.89%) bins.
Finished parsing hits for 4 of 38 (10.53%) bins.
Finished parsing hits for 5 of 38 (13.16%) bins.
Finished parsing hits for 6 of 38 (15.79%) bins.
Finished parsing hits for 7 of 38 (18.42%) bins.
Finished parsing hits for 8 of 38 (21.05%) bins.
Finished parsing hits for 9 of 38 (23.68%) bins.
Finished parsing hits for 10 of 38 (26.32%) bins.
Finished parsing hits for 11 of 38 (28.95%) bins.
Finished parsing hits for 12 of 38 (31.58%) bins.
Finished parsing hits for 13 of 38 (34.21%) bins.
Finished parsing hits for 14 of 38 (36.84%) bins.
Finished parsing hits for 15 of 38 (39.47%) bins.
Finished parsing hits for 16 of 38 (42.11%) bins.
Finished parsing hits for 17 of 38 (44.74%) bins.
Finished parsing hits for 18 of 38 (47.37%) bins.
Finished parsing hits for 19 of 38 (50.00%) bins.
Finished parsing hits for 20 of 38 (52.63%) bins.
Finished parsing hits for 21 of 38 (55.26%) bins.
Finished parsing hits for 22 of 38 (57.89%) bins.
Finished parsing hits for 23 of 38 (60.53%) bins.
Finished parsing hits for 24 of 38 (63.16%) bins.
Finished parsing hits for 25 of 38 (65.79%) bins.
Finished parsing hits for 26 of 38 (68.42%) bins.
Finished parsing hits for 27 of 38 (71.05%) bins.
Finished parsing hits for 28 of 38 (73.68%) bins.
Finished parsing hits for 29 of 38 (76.32%) bins.
Finished parsing hits for 30 of 38 (78.95%) bins.
Finished parsing hits for 31 of 38 (81.58%) bins.
Finished parsing hits for 32 of 38 (84.21%) bins.
Finished parsing hits for 33 of 38 (86.84%) bins.
Finished parsing hits for 34 of 38 (89.47%) bins.
Finished parsing hits for 35 of 38 (92.11%) bins.
Finished parsing hits for 36 of 38 (94.74%) bins.
Finished parsing hits for 37 of 38 (97.37%) bins.
Finished parsing hits for 38 of 38 (100.00%) bins.
Aligning marker genes with multiple hits in a single bin:
Finished processing 0 of 38 (0.00%) bins.
Finished processing 1 of 38 (2.63%) bins.
Finished processing 2 of 38 (5.26%) bins.
Finished processing 3 of 38 (7.89%) bins.
Finished processing 4 of 38 (10.53%) bins.
Finished processing 5 of 38 (13.16%) bins.
Finished processing 6 of 38 (15.79%) bins.
Finished processing 7 of 38 (18.42%) bins.
Finished processing 8 of 38 (21.05%) bins.
Finished processing 9 of 38 (23.68%) bins.
Finished processing 10 of 38 (26.32%) bins.
Finished processing 11 of 38 (28.95%) bins.
Finished processing 12 of 38 (31.58%) bins.
Finished processing 13 of 38 (34.21%) bins.
Finished processing 14 of 38 (36.84%) bins.
Finished processing 15 of 38 (39.47%) bins.
Finished processing 16 of 38 (42.11%) bins.
Finished processing 17 of 38 (44.74%) bins.
Finished processing 18 of 38 (47.37%) bins.
Finished processing 19 of 38 (50.00%) bins.
Finished processing 20 of 38 (52.63%) bins.
Finished processing 21 of 38 (55.26%) bins.
Finished processing 22 of 38 (57.89%) bins.
Finished processing 23 of 38 (60.53%) bins.
Finished processing 24 of 38 (63.16%) bins.
Finished processing 25 of 38 (65.79%) bins.
Finished processing 26 of 38 (68.42%) bins.
Finished processing 27 of 38 (71.05%) bins.
Finished processing 28 of 38 (73.68%) bins.
Finished processing 29 of 38 (76.32%) bins.
Finished processing 30 of 38 (78.95%) bins.
Finished processing 31 of 38 (81.58%) bins.
Finished processing 32 of 38 (84.21%) bins.
Finished processing 33 of 38 (86.84%) bins.
Finished processing 34 of 38 (89.47%) bins.
Finished processing 35 of 38 (92.11%) bins.
Finished processing 36 of 38 (94.74%) bins.
Finished processing 37 of 38 (97.37%) bins.
Finished processing 38 of 38 (100.00%) bins.
{ Current stage: 0:00:09.718 || Total: 0:10:35.836 }
Calculating genome statistics for 38 bins with 40 threads:
Finished processing 0 of 38 (0.00%) bins.
Finished processing 1 of 38 (2.63%) bins.
Finished processing 2 of 38 (5.26%) bins.
Finished processing 3 of 38 (7.89%) bins.
Finished processing 4 of 38 (10.53%) bins.
Finished processing 5 of 38 (13.16%) bins.
Finished processing 6 of 38 (15.79%) bins.
Finished processing 7 of 38 (18.42%) bins.
Finished processing 8 of 38 (21.05%) bins.
Finished processing 9 of 38 (23.68%) bins.
Finished processing 10 of 38 (26.32%) bins.
Finished processing 11 of 38 (28.95%) bins.
Finished processing 12 of 38 (31.58%) bins.
Finished processing 13 of 38 (34.21%) bins.
Finished processing 14 of 38 (36.84%) bins.
Finished processing 15 of 38 (39.47%) bins.
Finished processing 16 of 38 (42.11%) bins.
Finished processing 17 of 38 (44.74%) bins.
Finished processing 18 of 38 (47.37%) bins.
Finished processing 19 of 38 (50.00%) bins.
Finished processing 20 of 38 (52.63%) bins.
Finished processing 21 of 38 (55.26%) bins.
Finished processing 22 of 38 (57.89%) bins.
Finished processing 23 of 38 (60.53%) bins.
Finished processing 24 of 38 (63.16%) bins.
Finished processing 25 of 38 (65.79%) bins.
Finished processing 26 of 38 (68.42%) bins.
Finished processing 27 of 38 (71.05%) bins.
Finished processing 28 of 38 (73.68%) bins.
Finished processing 29 of 38 (76.32%) bins.
Finished processing 30 of 38 (78.95%) bins.
Finished processing 31 of 38 (81.58%) bins.
Finished processing 32 of 38 (84.21%) bins.
Finished processing 33 of 38 (86.84%) bins.
Finished processing 34 of 38 (89.47%) bins.
Finished processing 35 of 38 (92.11%) bins.
Finished processing 36 of 38 (94.74%) bins.
Finished processing 37 of 38 (97.37%) bins.
Finished processing 38 of 38 (100.00%) bins.
{ Current stage: 0:00:00.408 || Total: 0:10:36.245 }
*******************************************************************************
[CheckM - qa] Tabulating genome statistics.
*******************************************************************************
Calculating AAI between multi-copy marker genes.
Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 38 (2.63%) bins.
Finished parsing hits for 2 of 38 (5.26%) bins.
Finished parsing hits for 3 of 38 (7.89%) bins.
Finished parsing hits for 4 of 38 (10.53%) bins.
Finished parsing hits for 5 of 38 (13.16%) bins.
Finished parsing hits for 6 of 38 (15.79%) bins.
Finished parsing hits for 7 of 38 (18.42%) bins.
Finished parsing hits for 8 of 38 (21.05%) bins.
Finished parsing hits for 9 of 38 (23.68%) bins.
Finished parsing hits for 10 of 38 (26.32%) bins.
Finished parsing hits for 11 of 38 (28.95%) bins.
Finished parsing hits for 12 of 38 (31.58%) bins.
Finished parsing hits for 13 of 38 (34.21%) bins.
Finished parsing hits for 14 of 38 (36.84%) bins.
Finished parsing hits for 15 of 38 (39.47%) bins.
Finished parsing hits for 16 of 38 (42.11%) bins.
Finished parsing hits for 17 of 38 (44.74%) bins.
Finished parsing hits for 18 of 38 (47.37%) bins.
Finished parsing hits for 19 of 38 (50.00%) bins.
Finished parsing hits for 20 of 38 (52.63%) bins.
Finished parsing hits for 21 of 38 (55.26%) bins.
Finished parsing hits for 22 of 38 (57.89%) bins.
Finished parsing hits for 23 of 38 (60.53%) bins.
Finished parsing hits for 24 of 38 (63.16%) bins.
Finished parsing hits for 25 of 38 (65.79%) bins.
Finished parsing hits for 26 of 38 (68.42%) bins.
Finished parsing hits for 27 of 38 (71.05%) bins.
Finished parsing hits for 28 of 38 (73.68%) bins.
Finished parsing hits for 29 of 38 (76.32%) bins.
Finished parsing hits for 30 of 38 (78.95%) bins.
Finished parsing hits for 31 of 38 (81.58%) bins.
Finished parsing hits for 32 of 38 (84.21%) bins.
Finished parsing hits for 33 of 38 (86.84%) bins.
Finished parsing hits for 34 of 38 (89.47%) bins.
Finished parsing hits for 35 of 38 (92.11%) bins.
Finished parsing hits for 36 of 38 (94.74%) bins.
Finished parsing hits for 37 of 38 (97.37%) bins.
Finished parsing hits for 38 of 38 (100.00%) bins.
{ Current stage: 0:00:11.233 || Total: 0:10:47.479 }
real 67m46.319s
user 459m13.198s
sys 6m55.175s
Thanks for that. However, I cant seem to find your original error in this output - rm: cannot removeINITIAL_BINNING/*checkm': No such file or directory`. Seems to me that the program finished flawlessly!
xiaochen2015
commented
5 years ago Yes，Thanks for your reply. the error rm: cannot removeINITIAL_BINNING/*checkm': No such file or directory` was corrected. Because I set a wrong configure of Checkm database, and now it was corrected.
The another question: In the output folder, I saw 4 folders：3 final bin sets and 1 work_files. but the file insert_sizes.txt did not exsist (in Usage_tutorial.md(https://github.com/bxlab/metaWRAP/blob/master/Usage_tutorial.md), the file 'insert_sizes.txt' is exists).
I didn't know why?
ursky
commented
5 years ago That feature was deprecated a few versions ago - it caused more issues than it was worth.
xiaochen2015
commented
5 years ago OK, I understood. Thank you very much!
Hi, I have run the binning module. I ran this order:
I get this error: rm: cannot remove `INITIAL_BINNING/*checkm': No such file or directory.
And this order was still finished. At last, " BINNING PIPELINE SUCCESSFULLY FINISHED!!!“ appeared in screen.
In the output folder, I saw 4 folders：3 final bin sets and 1 work_files. but the file 'insert_sizes.txt' did not exsist.
What may be the issue with this?
Thanks!