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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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ERROR: split master contig depth file into individual files when MaxBin2 binning #87

Open chen318liang opened 5 years ago

chen318liang commented 5 years ago

### when run the binning module, it successfully finished. But there is an error in the running. does it matters? the errors is below. thanks!

#####                                                RUNNING MAXBIN2                                               #####
########################################################################################################################

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-----                                          making contig depth file...                                         -----
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Output depth matrix to Zymo-GridION-EVEN_binning1/work_files/mb2_master_depth.txt
Calculating intra contig depth variance
Output matrix to Zymo-GridION-EVEN_binning1/work_files/mb2_master_depth.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: MC.bam with 6603812 reads and 6414944 readsWellMapped
Creating depth matrix file: Zymo-GridION-EVEN_binning1/work_files/mb2_master_depth.txt
Closing most bam files
Closing last bam file
Finished

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-----                    split master contig depth file into individual files for maxbin2 input                    -----
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processing MC.bam depth file...
readline() on closed filehandle FILE at **_/ELK2/wangjun/software/miniconda3/envs/metawrap/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...                                       -----
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readline() on closed filehandle FILE at /ELK2/wangjun/software/miniconda3/envs/metawrap/bin/run_MaxBin.pl line 1336.
MaxBin 2.2.4
Input contig: Zymo-GridION-EVEN_binning1/work_files/assembly.fa
Thread: 26
Min contig length: 1000
out header: Zymo-GridION-EVEN_binning1/work_files/maxbin2_out/bin
Located abundance file [/ELK2/wangjun/chenl/Zymo_Community_Standards_data/Zymo-GridION-EVEN_binning1/work_files/mb2_MC.txt]
Searching against 107 marker genes to find starting seed contigs for [Zymo-GridION-EVEN_binning1/work_files/assembly.fa]...
Running FragGeneScan....
Running HMMER hmmsearch....
Done data collection. Running MaxBin...
Command: /ELK2/wangjun/software/miniconda3/envs/metawrap/bin/src/MaxBin -fasta Zymo-GridION-EVEN_binning1/work_files/maxbin2_out/bin.contig.tmp  -abund Zymo-GridION-EVEN_binning1/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed Zymo-GridION-EVEN_binning1/work_files/maxbin2_out/bin.seed -out Zymo-GridION-EVEN_binning1/work_files/maxbin2_out/bin -min_contig_length 1000 -thread 26
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
        NODE_1_length_4752456_cov_19.170097 [26.346300]
……
ursky commented 5 years ago

This is the normal program behavior. If it finished fine then don't worry about it.

chen318liang commented 5 years ago

ok! thanks very much!