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Old 03-05-2017, 02:51 PM   #28
RubenD
Junior Member
 
Location: Boston

Join Date: Mar 2017
Posts: 3
Default how to change default bbsplit parameters?

Hi all,

I would like to use bbsplit to separate my fastq files.

First I generated an index and now I am running a for loop for all my fastq's.

However when I run the command it seems that the default parameter values are not changed, see for example parameters minhits and maxindel in bold below. Which parameter will it take?

Am I doing something wrong here?


Quote:
Merged reference file /gcdata/gcproj/Ruben/GENOMES/BBmap_indices/ref/genome/2/merged_ref_208959345802405.fa.gz already exists; skipping merge.
Ref merge time: 0.028 seconds.
Executing align2.BBMap [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, minhits=2, maxindel=200000, t=10, ambiguous=best, ambiguous2=best, build=2, in=../Fastq_files/20161223_CDX10_CC3737_S7_R1_001.fastq.gz, out_human=20161223_CDX10_CC3737_S7_R1_001_human.fastq, out_mouse=20161223_CDX10_CC3737_S7_R1_001_mouse.fastq, scafstats=scafstats_20161223_CDX10_CC3737_S7_R1_001.txt, refstats=refstats_20161223_CDX10_CC3737_S7_R1_001.txt, ref=/gcdata/gcproj/Ruben/GENOMES/BBmap_indices/ref/genome/2/merged_ref_208959345802405.fa.gz]

BBMap version 37.00
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.560
Set threads to 10
Scaffold statistics will be written to scafstats_20161223_CDX10_CC3737_S7_R1_001.txt
Reference set statistics will be written to refstats_20161223_CDX10_CC3737_S7_R1_001.txt
Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete /gcdata/gcproj/Ruben/GENOMES/BBmap_indices/ref/genome/2/summary.txt
Set genome to 2
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