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Old 05-18-2021, 10:03 AM   #1
floem7
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Location: Poland, Warsaw

Join Date: Jan 2013
Posts: 19
Question bbwrap.sh, is output OK?

Hi all,

I have a library sequenced two times in paierd-end mode.

I have used bbwrap.sh

~/bin/bbmap/bbwrap.sh -in1=hds1r1_09clean.fastq.gz,hds1r1_26clean.fastq.gz -in2=hds1r2_09clean.fastq.gz,hds1r2_26clean.fastq.gz path=/media/mj/c8e2ccd2-6313-4092-be34-46144891720f/agp_v5 unpigz=t pigz=t threads=24 -Xmx100g outm=s68_to_b73v5.bam showprogress=250000 statsfile=stats_s68_to_b73v5 covstats=covstats_s68_to_b73v5

If I understand correctly it is possible to provide paired files in -in and -in2

The procedure proceeded ok, like bbmap.sh, after processing the first pair it printed info, which I expected:

------------------ Results ------------------

Genome: 1
Key Length: 13
Max Indel: 16000
Minimum Score Ratio: 0.56
Mapping Mode: normal

Reads: 461959640
Mapped reads: 455488907
Mapped bases: 44824369462
Ref scaffolds: 685
Ref bases: 2182075994

Percent mapped: 98.599
Percent proper pairs: 80.240
Average coverage: 20.542
Average coverage with deletions: 27.430
Standard deviation: 111.219
Percent scaffolds with any coverage: 100.00
Percent of reference bases covered: 98.53

Total time: 393719.639 seconds.

And later:

Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, unpigz=t, pigz=t, threads=24, showprogress=250000, statsfile=stats_s68_to_b73v5, covstats=covstats_s68_to_b73v5, indexloaded=t, in=hds1r1_26clean.fastq.gz, in2=hds1r2_26clean.fastq.gz]
Version 38.90

Set threads to 24
Retaining first best site only for ambiguous mappings.
No output file.
Cleared Memory: 0.308 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 24 mapping threads.
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23

------------------ Results ------------------

Genome: 1
Key Length: 13
Max Indel: 16000
Minimum Score Ratio: 0.56
Mapping Mode: normal

Total time: 381683.967 seconds.


I'm surprised to see "No output file." in the messages above. Also the entire output ended with "total time" and no statistics as for the first read-pair.

So in the end I wonder if my resulting file is ok (I used outm to get only mapped reads). I.e. does it contain mapped reads from all four files?

I don't want to test if, for example merged file from separate runs of bbmap for both pairs would give the same number of mapped reads. It would take too much time.
bbwrap seems ok, but from my point of view it is not enough documented.
floem7 is offline   Reply With Quote