ARTIC workflow error during Realigh Read with samtools
PHemarajata opened this issue · comments
Hi, I ran in the the error below while running the ARTIC workflow during Realign Reads step:
sort: unrecognized option '--no-PG'
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
Any suggestion would be highly appreciated. Thank you!
@PHemarajata can you share with us your history?
Maybe it was a bit optimistic to not have an explicit samtools version 1.10 requirement as part of galaxyproject/tools-iuc#3077? The --no-PG option got added to samtools sort only at that version (1.9 and lower don't have it).
@PHemarajata which Galaxy server are you seeing this on (the tool is working fine on usegalaxy.org and usegalaxy.eu)?
@bgruening Could this have something to do with the conda channel order?
@bgruening Could this have something to do with the conda channel order?
I don't think so. But wherever this workflow is running we should check the samtools version.
I am running the workflow on my local Galaxy server. Since you guys were talking about versions, I tried changing the lofreq (for the Call Variants step) and lofreq viterbi (for the Realign Reads step) versions used in the workflow from 2.1.5 to 2.1.3.1 and the workflow was able to run to completion. I am so glad it worked. Thank you everyone for such a great tool.