Binning output directory

[DCossey]

Hello,

It seems that the output directories given to me by metawrap binning do not match the description in the documentation. I get a directory for each binner, but in these i have what appears to be the non-binned files. In the work_files I have the bin for only maxbin2. I ran this on a small subset of my data. I have put the command and all the output below:

metawrap binning -o /var/lib/minknow/data/pipeline_test/metawrap_test3 -t 25 -a /var/lib/minknow/data/pipeline_test/flye_test_barcode_01/assembly.fasta --metabat2 --maxbin2 --single-end --universal /var/lib/minknow/data/pipeline_test/fastq/EXP-PBC096_barcode01.fastq_filt.fastq
metawrap binning -o /var/lib/minknow/data/pipeline_test/metawrap_test3 -t 25 -a /var/lib/minknow/data/pipeline_test/flye_test_barcode_01/assembly.fasta --metabat2 --maxbin2 --single-end --universal /var/lib/minknow/data/pipeline_test/fastq/EXP-PBC096_barcode01.fastq_filt.fastq

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----- Entered read type: single -----

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ALIGNING READS TO MAKE COVERAGE FILES

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----- making copy of assembly file -----
----- /var/lib/minknow/data/pipeline_test/flye_test_barcode_01/assembly.fasta -----

---

----- Indexing assembly file -----

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.05 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/assembly.fa
[main] Real time: 0.078 sec; CPU: 0.069 sec

---

----- Aligning /var/lib/minknow/data/pipeline_test/fastq/EXP-PBC096_barcode01.fastq_filt.fastq -----
----- back to assembly, and sorting the alignment -----

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 44972 sequences (45438753 bp)...
[M::mem_process_seqs] Processed 44972 reads in 34.109 CPU sec, 1.375 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 25 /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/assembly.fa /var/lib/minknow/data/pipeline_test/fastq/EXP-PBC096_barcode01.fastq_filt.fastq
[main] Real time: 1.599 sec; CPU: 34.324 sec

---

----- Sorting the EXP-PBC096_barcode01.fastq_filt alignment file -----

[bam_sort_core] merging from 0 files and 25 in-memory blocks...

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RUNNING METABAT2

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----- making contig depth file... -----

Output depth matrix to /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/metabat_depth.txt
Output matrix to /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/metabat_depth.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: EXP-PBC096_barcode01.fastq_filt.bam with 49189 reads and 19864 readsWellMapped
Creating depth matrix file: /var/lib/minknow/data/pipeline_test/metawrap_test3/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.
0 bins (0 bases in total) formed.

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----- metaBAT2 finished successfully, and found 1 bins! -----

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RUNNING MAXBIN2

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----- making contig depth file... -----

Output depth matrix to /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/mb2_master_depth.txt
Calculating intra contig depth variance
Output matrix to /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/mb2_master_depth.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: EXP-PBC096_barcode01.fastq_filt.bam with 49189 reads and 19864 readsWellMapped
Creating depth matrix file: /var/lib/minknow/data/pipeline_test/metawrap_test3/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 EXP-PBC096_barcode01.fastq_filt.bam depth file...
MaxBin 2.2.6
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 2.2.6
Input contig: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/assembly.fa
Switch to 40 marker genes universal for bacteria and archaea.
Thread: 25
Min contig length: 1000
out header: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin
Located abundance file [/var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/mb2_EXP-PBC096_barcode01.fastq_filt.txt]
Searching against 40 marker genes to find starting seed contigs for [/var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/assembly.fa]...
Running FragGeneScan....
Running HMMER hmmsearch....
Try harder to dig out marker genes from contigs.
Done data collection. Running MaxBin...
Command: /home/tanentzap/miniconda3/envs/metawrap-env/opt/MaxBin-2.2.6/src/MaxBin -fasta /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.contig.tmp -abund /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.contig.tmp.abund1 -seed /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.seed -out /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin -min_contig_length 1000 -thread 25
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
contig_48 [4.913920]
contig_75 [314.327000]
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

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.001.marker.fasta
Deleting intermediate files.

========== Job finished ==========
Yielded 1 bins for contig (scaffold) file /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/assembly.fa

Here are the output files for this run.
Please refer to the README file for further details.

Summary file: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.summary
Marker counts: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.marker
Marker genes for each bin: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.marker_of_each_gene.tar.gz
Bin files: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.001.fasta - /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.001.fasta
Unbinned sequences: /var/lib/minknow/data/pipeline_test/metawrap_test3/work_files/maxbin2_out/bin.noclass

========== Elapsed Time ==========
0 hours 0 minutes and 1 seconds.

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----- MaxBin2 finished successfully, and found 1 bins! -----

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BINNING PIPELINE SUCCESSFULLY FINISHED!!!

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real 0m3.914s
user 0m40.098s
sys 0m1.473s