Parameter 'stats2' in rqcfilter2.sh is not recognized
BBMap short read aligner, and other bioinformatic tools.
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brian-jgi
When using rqcfilter2.sh, I learned we can use a parameter "stats2=filterStats2.txt" to generate better overall stats, based on the help message:
stats=filterStats.txt Overall stats file name.
stats2=filterStats2.txt Better overall stats file name.
However, when I added this parameter in my command, it produced an error, and I believe the reason is that this parameter was somehow passed to BBDuk and BBDuck doesen't have this option. Please see the error message below:
Memory: max=101362m, total=101362m, free=101345m, used=17m
Executing jgi.BBDuk [ktrim=r, ordered, minlen=51, minlenfraction=0.33, mink=11, tbo, tpe, rcomp=f, overwrite=true, k=23, hdist=1, hdist2=1, ftm=5, pratio=G,C, plen=20, phist=phist.txt, qhist=qhist.txt, bhist=bhist.txt, gchist=gchist.txt, pigz=t, unpigz=t, zl=4, Xmx=100000m, stats2=E1-1-5_.rqdfilter2.filterStats2.txt, ow=true, in1=/tmp/pbs.1789479.aqua/TEMP_FBT_3c3c71696e021f1bd4c36b2a05bf5_E1-1-5_clean_1.fastq.gz, in2=/tmp/pbs.1789479.aqua/TEMP_FBT_3c3c71696e021f1bd4c36b2a05bf5_E1-1-5_clean_2.fastq.gz, out1=/tmp/pbs.1789479.aqua/TEMP_TRIM_3c3c71696e021f1bd4c36b2a05bf5_E1-1-5_clean_1.fastq.gz, out2=/tmp/pbs.1789479.aqua/TEMP_TRIM_3c3c71696e021f1bd4c36b2a05bf5_E1-1-5_clean_2.fastq.gz, rqc=hashmap, outduk=ktrim_kmerStats1.txt, stats=ktrim_scaffoldStats1.txt, loglog, loglogout, ref=/mnt/hpccs01/work/microbiome/users/heyu/db/BBTools_res/RQCFilterData/adapters2.fa.gz]
Version 39.19
Set quality histogram output to qhist.txt
Set base content histogram output to bhist.txt
Set GC histogram output to gchist.txt
Exception in thread "main" java.lang.RuntimeException: Unknown parameter stats2=E1-1-5_.rqdfilter2.filterStats2.txt
at jgi.BBDuk.<init>(BBDuk.java:566)
at jgi.RQCFilter2.ktrim(RQCFilter2.java:2119)
at jgi.RQCFilter2.process(RQCFilter2.java:1084)
at jgi.RQCFilter2.main(RQCFilter2.java:73)
That's odd; looks to me like it should be working. What version are you using?
hi Brian, thanks for the reply. It's the newest version - 39.19. I just deployed it by conda yesterday.
OK! I'll look into it and get back to you.
Found the problem in the parser; it will be fixed in 39.20.
Great. Thank you Brian!