Open JinqunHuang opened 5 years ago
ursky
commented
5 years ago Since I am seeing the INITIAL_BINNING/work_files/concoct_out exists warning, it is possible that this is caused by intermediate concoct files from a previous run. Can you deliberately delete INITIAL_BINNING/work_files/concoct_out and see what happens?
Other than that, you could try to update metawrap to get the more recent concoct v1.0, which may be better for you anyways.
JinqunHuang
commented
5 years ago Drer Uritskiy,
Thank you for replying so quickly.
Now I'm intalling the metawrap-mg=1.1.6 and see what happen.
Thank you again for your help.
sincerely,
JinQun Huang
发件人: Gherman V. Uritskiy notifications@github.com 发送时间: 2019年3月27日 21:04 收件人: bxlab/metaWRAP 抄送: 黄锦群(Jinqun Huang); Author 主题: Re: [bxlab/metaWRAP] Something went wrong with binning with CONCOCT. metawrap-modules/binning.sh: line 421: 29910 Segmentation fault (#150)
Since I am seeing the INITIAL_BINNING/work_files/concoct_out exists warning, it is possible that this is caused by intermediate concoct files from a previous run. Can you deliberately delete INITIAL_BINNING/work_files/concoct_out and see what happens?
Other than that, you could try to update metawrap to get the more recent concoct v1.0, which may be better for you anyways.
― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/bxlab/metaWRAP/issues/150#issuecomment-477143343, or mute the threadhttps://github.com/notifications/unsubscribe-auth/As9I4-vt-0QxTc8zPzXiDLQc8GZ5Wg9jks5va2xBgaJpZM4cNCbq.
JinqunHuang
commented
5 years ago @ursky Drer Uritskiy,
I install metawrap 1.1.8 by commands as below:
conda activate metawrap-env
conda install -y -c ursky metawrap-mg=1.1.8Then I run bining step:
conda activate metawrap-env
metawrap binning -o INITIAL_BINNING -t 8 -a contigs.fasta.2000.fasta --metabat2 --maxbin2 --concoct Reads.AS101.wHAXPI037952-71_1.fastq Reads.AS101.wHAXPI037952-71_2.fastqIt runs successfully in MATABAT2, but I got the error in MAXBIN2. however, It runs successfully in CONCOCT by this version.
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 8 INITIAL_BINNING/work_files/assembly.fa Reads.AS101.wHAXPI037952-71_1.fastq Reads.AS101.wHAXPI037952-71_2.fastq
[main] Real time: 1813.472 sec; CPU: 7365.346 sec
------------------------------------------------------------------------------------------------------------------------
----- Sorting the Reads.AS101.wHAXPI037952-71 alignment file -----
------------------------------------------------------------------------------------------------------------------------
[bam_sort_core] merging from 16 files and 8 in-memory blocks...
########################################################################################################################
##### RUNNING METABAT2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
Output depth matrix to INITIAL_BINNING/work_files/metabat_depth.txt
Output matrix to INITIAL_BINNING/work_files/metabat_depth.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: Reads.AS101.wHAXPI037952-71.bam with 49225306 reads and 44950126 readsWellMapped
Creating depth matrix file: INITIAL_BINNING/work_files/metabat_depth.txt
Closing most bam files
Closing last bam file
Finished
------------------------------------------------------------------------------------------------------------------------
----- 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.
74 bins (82841173 bases in total) formed.
------------------------------------------------------------------------------------------------------------------------
----- metaBAT2 finished successfully, and found 75 bins! -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### RUNNING MAXBIN2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
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 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: Reads.AS101.wHAXPI037952-71.bam with 49225306 reads and 44950126 readsWellMapped
Creating depth matrix file: INITIAL_BINNING/work_files/mb2_master_depth.txt
Closing most bam files
Closing last bam file
Finished
------------------------------------------------------------------------------------------------------------------------
----- split master contig depth file into individual files for maxbin2 input -----
------------------------------------------------------------------------------------------------------------------------
processing Reads.AS101.wHAXPI037952-71.bam depth file...
readline() on closed filehandle FILE at miniconda2/envs/metawrap-env/bin/run_MaxBin.pl line 1336.
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... -----
------------------------------------------------------------------------------------------------------------------------
readline() on closed filehandle FILE at miniconda2/envs/metawrap-env/bin/run_MaxBin.pl line 1336.
MaxBin 2.2.4
Input contig: INITIAL_BINNING/work_files/assembly.fa
Thread: 8
Min contig length: 1000
out header: INITIAL_BINNING/work_files/maxbin2_out/bin
Located abundance file [INITIAL_BINNING/work_files/mb2_Reads.AS101.wHAXPI037952-71.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: miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp -abund INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed INITIAL_BINNING/work_files/maxbin2_out/bin.seed -out INITIAL_BINNING/work_files/maxbin2_out/bin -min_contig_length 1000 -thread 8
miniconda2/envs/metawrap-env/bin/src/MaxBin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by miniconda2/envs/metawrap-env/bin/src/MaxBin)
Error encountered while running core MaxBin program. Error recorded in INITIAL_BINNING/work_files/maxbin2_out/bin.log.
Program Stop.
************************************************************************************************************************
***** Something went wrong with running MaxBin2. Exiting. *****
************************************************************************************************************************
real 61m8.014s
user 158m24.106s
sys 3m49.110sI Configure the glibc-2.14, then maxbin2 runs successfully. It may be a bug in the package with 1.1.8 version and previous versions. metawrap binning -o INITIAL_BINNING -t 8 -a contigs.fasta.2000.fasta --maxbin2 Reads.AS100.wHAXPI037951-70_1.fastq Reads.AS100.wHAXPI037951-70_2.fastq
it should be noted that, glibc-2.14 should be Configured before running "metawrap binning --maxbin2", but shouldn't be Configured before running "Aligning fastq to assembly". It may cause the bwa mapping problem.
prefix=/share/app/glibc-2.14/ export PATH=$prefix/bin:$PATH export MANPATH=$prefix/man:$MANPATH export LD_LIBRARY_PATH=$prefix/lib:$prefix/lib64:$LD_LIBRARY_PATH export CFLAGS="-I$prefix/include" export LDFLAGS="-L$prefix/lib" export C_INCLUDE_PATH=$C_INCLUDE_PATH:$prefix/include export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$prefix/include
ursky
commented
5 years ago The issue seems to stem from conda's MaxBin2 using your system's /lib64/libc.so.6 instead of the one in the env. Thanks for posting the fix. Just to be clear though, you are forcing the programs to use your system's libraries rather than conda's. Can you try running conda install -c bcbio glibc to install libc.so.6 into your env instead, and see if that fixes it?
JinqunHuang
commented
5 years ago conda activate metawrap-env
conda install -c bcbio glibc
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- glibcso, I run commands as below, and the glibc214 install successfully.
conda activate metawrap-env
conda install -c pwwang glibc214But it get the same errors in MaxBin2.
conda activate metawrap-env
metawrap binning -o INITIAL_BINNING -t 8 -a contigs.fasta.2000 --maxbin2 Reads.AS102.wHAXPI037953-72_1.fastq Reads.AS102.wHAXPI037953-72_2.fastq
...
########################################################################################################################
##### RUNNING MAXBIN2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
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 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: Reads.AS102.wHAXPI037953-72.bam with 48164946 reads and 42123995 readsWellMapped
Creating depth matrix file: INITIAL_BINNING/work_files/mb2_master_depth.txt
Closing most bam files
Closing last bam file
Finished
------------------------------------------------------------------------------------------------------------------------
----- split master contig depth file into individual files for maxbin2 input -----
------------------------------------------------------------------------------------------------------------------------
processing Reads.AS102.wHAXPI037953-72.bam depth file...
readline() on closed filehandle FILE at /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/run_MaxBin.pl line 1336.
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... -----
------------------------------------------------------------------------------------------------------------------------
readline() on closed filehandle FILE at /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/run_MaxBin.pl line 1336.
MaxBin 2.2.4
Input contig: INITIAL_BINNING/work_files/assembly.fa
Thread: 8
Min contig length: 1000
out header: INITIAL_BINNING/work_files/maxbin2_out/bin
Located abundance file [/hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS102/INITIAL_BINNING/work_files/mb2_Reads.AS102.wHAXPI037953-72.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: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp -abund INITIAL_BINNING/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed INITIAL_BINNING/work_files/maxbin2_out/bin.seed -out INITIAL_BINNING/work_files/maxbin2_out/bin -min_contig_length 1000 -thread 8
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin)
Error encountered while running core MaxBin program. Error recorded in INITIAL_BINNING/work_files/maxbin2_out/bin.log.
Program Stop.
************************************************************************************************************************
***** Something went wrong with running MaxBin2. Exiting. *****
************************************************************************************************************************
real 35m8.832s
user 143m59.416s
sys 3m45.803sI am unfamiliar with that package. Can you check if libc.so.6 is in your miniconda2/envs/metawrap-env/lib/?
JinqunHuang
commented
5 years ago I could not find libc.so.6 is in miniconda2/envs/metawrap-env/lib/
This makes me wonder, I actually install glibc214 in metawrap-env
conda activate metawrap-env conda install -c pwwang glibc214
ursky
commented
5 years ago I think i gave you the wrong source. Try conda install -c asmeurer glibc. That should install a copy of libc.so.6. Or if that fails try conda install -c dan_blanchard glibc.
JinqunHuang
commented
5 years ago After I install glibc by -c dan_blanchard or -c asmeurerchannel, I can find the miniconda2/envs/metawrap-env/lib/libc.so.6.
But both packages of glibc could not work successfully. The program request glibc-2.14, but the both packages were not this version and may be cause the problem.
conda activate metawrap-env
metawrap binning -o INITIAL_BINNING -t 8 -a contigs.fasta.2000 --maxbin2 /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS102/Reads.AS102.wHAXPI037953-72_1.fastq /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS102/Reads.AS102.wHAXPI037953-72_2.fastq
metawrap binning -o INITIAL_BINNING -t 8 -a contigs.fasta.2000 --maxbin2 /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS102/Reads.AS102.wHAXPI037953-72_1.fastq /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS102/Reads.AS102.wHAXPI037953-72_2.fastq
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 45: 25878 Segmentation fault ${SOFT}/print_comment.py "$1" "-"
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 45: 25903 Segmentation fault ${SOFT}/print_comment.py "$1" "-"
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 48: 25904 Segmentation fault ${SOFT}/print_comment.py "$1" "#"
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 45: 25909 Segmentation fault ${SOFT}/print_comment.py "$1" "-"
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 45: 26009 Segmentation fault ${SOFT}/print_comment.py "$1" "-"
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 216: 26012 Segmentation fault bwa index ${out}/work_files/assembly.fa
/hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/metawrap-modules/binning.sh: line 46: 26014 Segmentation fault ${SOFT}/print_comment.py "$1" "*"
real 0m4.401s
user 0m0.019s
sys 0m0.218sWait, I am confused - the new error is completely different? Looks like metawrap cant use the print functions in the metawrap installation, which might mean there is something wrong with the config-metawrap file (or its not in the PATH).
JinqunHuang
commented
5 years ago I do not change the ${SOFT} in the config-metawrap file.
Finally, I uninstall the glibc in conda, and force the program using the glibc214 libraries which I installed. And Maxbin2 can still run successfully, and the "Segmentation fault ${SOFT}/print_comment.py $1" do not appear.
Is there anything else I can test for you?
ursky
commented
5 years ago No, thank you! Hopefully this will be useful for others with the same issue. Unfortunate that there is no easy fix yet.
JinqunHuang
commented
5 years ago Dear Gherman,
I run maxbin2 with metawrap 1.2.
I get some error in the step of "split master contig" and "Starting binning with MaxBin2".
Could you please give me some advices ? Thanks again.
Best, JinQun Huang
prefix=/share/app/glibc-2.14/
export PATH=$prefix/bin:$PATH
export MANPATH=$prefix/man:$MANPATH
export LD_LIBRARY_PATH=$prefix/lib:$prefix/lib64:$LD_LIBRARY_PATH
export CFLAGS="-I$prefix/include"
export LDFLAGS="-L$prefix/lib"
export C_INCLUDE_PATH=$C_INCLUDE_PATH:$prefix/include
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$prefix/include
$ metawrap binning -o /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning -t 1 -a /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/3.Individual_Assemble/AS103/contigs.fasta --maxbin2 -l 2000 /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS103/Reads.AS103.wHAXPI037955-142_1.fastq /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS103/Reads.AS103.wHAXPI037955-142_2.fastq
metawrap binning -o /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning -t 1 -a /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/3.Individual_Assemble/AS103/contigs.fasta --maxbin2 -l 2000 /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS103/Reads.AS103.wHAXPI037955-142_1.fastq /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/1.Clean_data/Upload/BGI_result/1.CleanDataAssess/CleanData/AS103/Reads.AS103.wHAXPI037955-142_2.fastq
------------------------------------------------------------------------------------------------------------------------
----- Entered read type: paired -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- 1 forward and 1 reverse read files detected -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### ALIGNING READS TO MAKE COVERAGE FILES #####
########################################################################################################################
Warning: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning already exists.
rm: cannot remove `/hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/*checkm': No such file or directory
------------------------------------------------------------------------------------------------------------------------
----- Looks like the assembly file is already coppied. Skipping... -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- Looks like there is a index of the assembly already. Skipping... -----
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
----- skipping aligning Reads.AS103.wHAXPI037955-142 reads to assembly because -----
----- /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/Reads.AS103.wHAXPI037955-142.bam -----
----- already exists. -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### RUNNING MAXBIN2 #####
########################################################################################################################
------------------------------------------------------------------------------------------------------------------------
----- making contig depth file... -----
------------------------------------------------------------------------------------------------------------------------
Output depth matrix to /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/mb2_master_depth.txt
Calculating intra contig depth variance
Output matrix to /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/mb2_master_depth.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: Reads.AS103.wHAXPI037955-142.bam with 48321634 reads and 46351604 readsWellMapped
Creating depth matrix file: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/mb2_master_depth.txt
Closing most bam files
Closing last bam file
Finished
------------------------------------------------------------------------------------------------------------------------
----- split master contig depth file into individual files for maxbin2 input -----
------------------------------------------------------------------------------------------------------------------------
processing Reads.AS103.wHAXPI037955-142.bam depth file...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
readline() on closed filehandle FILE at /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/run_MaxBin.pl line 1336.
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... -----
------------------------------------------------------------------------------------------------------------------------
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
readline() on closed filehandle FILE at /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/run_MaxBin.pl line 1336.
MaxBin 2.2.4
Input contig: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/assembly.fa
Thread: 1
Min contig length: 2000
out header: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin
Located abundance file [/hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/mb2_Reads.AS103.wHAXPI037955-142.txt]
Searching against 107 marker genes to find starting seed contigs for [/hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/assembly.fa]...
Running FragGeneScan....
Running HMMER hmmsearch....
Done data collection. Running MaxBin...
Command: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp -abund /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.seed -out /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin -min_contig_length 2000
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_22_length_255366_cov_4.849169 [31.377000]
NODE_34_length_210926_cov_20.206054 [131.447000]
NODE_35_length_209857_cov_3.085095 [19.990400]
NODE_65_length_152858_cov_2.761430 [17.913900]
NODE_87_length_133100_cov_6.681281 [43.212100]
NODE_192_length_82340_cov_35.173817 [228.825000]
NODE_194_length_81760_cov_44.525486 [283.105000]
NODE_234_length_71057_cov_8.385239 [54.299300]
NODE_244_length_69221_cov_19.731786 [128.725000]
NODE_295_length_58149_cov_4.064234 [26.379700]
NODE_387_length_48327_cov_1.481141 [9.658510]
NODE_442_length_43406_cov_1.536426 [9.927390]
NODE_469_length_41513_cov_1.750012 [11.383600]
NODE_475_length_40604_cov_1.568990 [10.231300]
NODE_559_length_35106_cov_1.717945 [11.187600]
NODE_648_length_30485_cov_51.037420 [318.278000]
NODE_759_length_26514_cov_10.308106 [66.764800]
NODE_865_length_23357_cov_1.808050 [11.950600]
NODE_1237_length_16258_cov_2.709689 [17.496800]
NODE_1488_length_13187_cov_1.289587 [8.647690]
NODE_1493_length_13130_cov_1.118434 [7.244530]
NODE_1657_length_11846_cov_2.280143 [14.776200]
NODE_1860_length_10495_cov_51.756752 [245.864000]
NODE_2337_length_8205_cov_1.184080 [7.919930]
NODE_2771_length_6737_cov_1.042814 [6.766210]
NODE_3373_length_5359_cov_2.064602 [15.933000]
NODE_3878_length_4659_cov_1.199691 [8.062540]
NODE_5002_length_3627_cov_0.712571 [4.811040]
NODE_7467_length_2508_cov_0.700966 [4.576340]
NODE_7661_length_2448_cov_0.831969 [5.356400]
Get 30 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: 127 (1.32%)
Elapsed time: 0 days 00:05:21
Done data collection. Running MaxBin...
Command: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0011.fasta -abund /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0011.out.seed -out /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0011.out -min_contig_length 2000
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_2011_length_9651_cov_1.852688 [12.253100]
NODE_9628_length_2004_cov_0.561002 [3.528590]
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
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: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0014.fasta -abund /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0014.out.seed -out /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0014.out -min_contig_length 2000
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_868_length_23221_cov_1.738417 [11.231800]
NODE_1992_length_9773_cov_0.994505 [6.537980]
NODE_5494_length_3310_cov_0.870562 [5.830700]
Get 3 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
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: 23 (1.95%)
Elapsed time: 0 days 00:00:04
Done data collection. Running MaxBin...
Command: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0015.fasta -abund /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0015.out.seed -out /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0015.out -min_contig_length 2000
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_848_length_23731_cov_1.341722 [8.716040]
NODE_1092_length_18395_cov_1.460696 [9.584870]
NODE_6469_length_2846_cov_0.904744 [5.784120]
Get 3 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: 72 (6.47%)
Elapsed time: 0 days 00:00:06
Done data collection. Running MaxBin...
Command: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0023.fasta -abund /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0023.out.seed -out /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0023.out -min_contig_length 2000
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_194_length_81760_cov_44.525486 [283.105000]
NODE_1860_length_10495_cov_51.756752 [245.864000]
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
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: /hwfssz4/BC_COM_FP/BC_CCP/Micro/software/miniconda2/envs/metawrap-env/bin/src/MaxBin -fasta /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0015.out.0003.fasta -abund /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0015.out.0003.out.seed -out /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.0015.out.0003.out -min_contig_length 2000
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_848_length_23731_cov_1.341722 [8.716040]
NODE_6469_length_2846_cov_0.904744 [5.784120]
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
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 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_22_length_255366_cov_4.849169 [31.377000]
NODE_34_length_210926_cov_20.206054 [131.447000]
NODE_35_length_209857_cov_3.085095 [19.990400]
NODE_65_length_152858_cov_2.761430 [17.913900]
NODE_87_length_133100_cov_6.681281 [43.212100]
NODE_192_length_82340_cov_35.173817 [228.825000]
NODE_194_length_81760_cov_44.525486 [283.105000]
NODE_234_length_71057_cov_8.385239 [54.299300]
NODE_244_length_69221_cov_19.731786 [128.725000]
NODE_295_length_58149_cov_4.064234 [26.379700]
NODE_387_length_48327_cov_1.481141 [9.658510]
NODE_442_length_43406_cov_1.536426 [9.927390]
NODE_469_length_41513_cov_1.750012 [11.383600]
NODE_475_length_40604_cov_1.568990 [10.231300]
NODE_559_length_35106_cov_1.717945 [11.187600]
NODE_648_length_30485_cov_51.037420 [318.278000]
NODE_759_length_26514_cov_10.308106 [66.764800]
NODE_865_length_23357_cov_1.808050 [11.950600]
NODE_1237_length_16258_cov_2.709689 [17.496800]
NODE_1488_length_13187_cov_1.289587 [8.647690]
NODE_1493_length_13130_cov_1.118434 [7.244530]
NODE_1657_length_11846_cov_2.280143 [14.776200]
NODE_1860_length_10495_cov_51.756752 [245.864000]
NODE_2337_length_8205_cov_1.184080 [7.919930]
NODE_2771_length_6737_cov_1.042814 [6.766210]
NODE_3373_length_5359_cov_2.064602 [15.933000]
NODE_3878_length_4659_cov_1.199691 [8.062540]
NODE_5002_length_3627_cov_0.712571 [4.811040]
NODE_7467_length_2508_cov_0.700966 [4.576340]
NODE_7661_length_2448_cov_0.831969 [5.356400]
Get 30 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: 127 (1.32%)
Elapsed time: 0 days 00:05:21
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_2011_length_9651_cov_1.852688 [12.253100]
NODE_9628_length_2004_cov_0.561002 [3.528590]
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
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 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_868_length_23221_cov_1.738417 [11.231800]
NODE_1992_length_9773_cov_0.994505 [6.537980]
NODE_5494_length_3310_cov_0.870562 [5.830700]
Get 3 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
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: 23 (1.95%)
Elapsed time: 0 days 00:00:04
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_848_length_23731_cov_1.341722 [8.716040]
NODE_1092_length_18395_cov_1.460696 [9.584870]
NODE_6469_length_2846_cov_0.904744 [5.784120]
Get 3 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: 72 (6.47%)
Elapsed time: 0 days 00:00:06
Minimum contig length set to 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_194_length_81760_cov_44.525486 [283.105000]
NODE_1860_length_10495_cov_51.756752 [245.864000]
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
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 2000.
Reading seed list...
Looking for seeds in sequences.
NODE_848_length_23731_cov_1.341722 [8.716040]
NODE_6469_length_2846_cov_0.904744 [5.784120]
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
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
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
bin.014.marker.fasta
bin.015.marker.fasta
bin.016.marker.fasta
bin.017.marker.fasta
bin.018.marker.fasta
bin.019.marker.fasta
bin.020.marker.fasta
bin.021.marker.fasta
bin.022.marker.fasta
bin.023.marker.fasta
bin.024.marker.fasta
bin.025.marker.fasta
bin.026.marker.fasta
bin.027.marker.fasta
bin.028.marker.fasta
bin.029.marker.fasta
bin.030.marker.fasta
bin.031.marker.fasta
bin.032.marker.fasta
bin.033.marker.fasta
bin.034.marker.fasta
bin.035.marker.fasta
bin.036.marker.fasta
bin.037.marker.fasta
Deleting intermediate files.
========== Job finished ==========
Yielded 37 bins for contig (scaffold) file /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/assembly.fa
Here are the output files for this run.
Please refer to the README file for further details.
Summary file: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.summary
Marker counts: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.marker
Marker genes for each bin: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.marker_of_each_gene.tar.gz
Bin files: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.001.fasta - /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.037.fasta
Unbinned sequences: /hwfssz6/BC_TS_DA/F16HTSSCWLJ0092/HUMdcwM/5.bining/AS103/binning/work_files/maxbin2_out/bin.noclass
========== Elapsed Time ==========
0 hours 14 minutes and 11 seconds.
------------------------------------------------------------------------------------------------------------------------
----- MaxBin2 finished successfully, and found 37 bins! -----
------------------------------------------------------------------------------------------------------------------------
########################################################################################################################
##### BINNING PIPELINE SUCCESSFULLY FINISHED!!! #####
########################################################################################################################
real 16m14.436s
user 13m40.847s
sys 0m42.409s
Dear friends: I run CONCOCT from MetaWRAP v=1.1.3. I have no idea how to debug this error. Please help me. Here is the command: