# Tagged with #parallel 0 documentation articles | 0 announcements | 2 forum discussions

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Created 2013-03-19 20:08:23 | Updated | Tags: parallel blip compression exception

Trying to run

java -jar $GATKJAR -R$REF -T UnifiedGenotyper -I file1.bam -I file2.bam -I file3.bam -glm BOTH -o output.vcf.gz


gives an error like:

 ##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR
##### ERROR MESSAGE: There was a failure because temporary file /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub1033673347640679118.tmp could not be found while running the GATK with more than one thread.  Possible causes for this problem include: your system's open file handle limit is too small, your output or temp directories do not have sufficient space, or just an isolated file system blip
##### ERROR ------------------------------------------------------------------------------------------


The file is actually there, and is gzip-compressed and vcf-formatted.

However, if I specify -o output.vcf instead of -o output.vcf.gz, then everything works. I suspect the problem is with the autodetection of the codec. In VariantContextWriterStorage, LocalParallelizationProblem is thrown not only if the tmp file cannot be found, but whenever a FeatureDescriptor cannot be found for the file.

So... It seems like compressed output cannot be used from threaded processing with UnifiedGenotyper. Is my assessment correct?

1. A better error message would be helpful to prevent others from trying the same thing I did.
2. It would be nice to be able to write compressed output from a threaded UnifiedGenotyper, perhaps: a) the temp file could be written uncompressed even though the final file will be compressed, or b) the Codec-detection could detect gzip-compressed files?

Created 2012-08-01 23:26:12 | Updated 2012-08-01 23:26:12 | Tags: reducereads parallel

I'm working with ReduceReads and would like to use it in some kind of parallel mode. The presentation mentions that a 50x way run may drastically reduce run time but I'm not sure how to invoke this. I tried -nt and it complained. Should I be giving it multiple intervals and merging? If so, how does it deal with edge variants?

Thanks.