GATK UnifiedGenotyper stuck, creates bamschedule.*.tmp files, no info in the logs
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Hi guys,

I have Googled my problem, with no luck, so I am asking you directly.

I am currently testing an established pipeline on BAMs from a new source, so I advance step by step, and the last step, the calling with UG, seems to have trouble.

My BAM endured, in order, Picard AddOrReplaceReadGroup, Picard MarkDup, GATK RealignerTargetCreator, GATK IndelRealigner, Picard FixMateInformation, GATK BaseRecalibrator, GATK PrintReads.

Arrived at UG, this is my (stuck) output (I removed file names because of privacy):

INFO 14:54:29,692 ArgumentTypeDescriptor - Dynamically determined type of /scratch/appli57_local_duplicates/reference/exome_target_intervals.bed to be BED INFO 14:54:29,748 HelpFormatter - --------------------------------------------------------------------------------- INFO 14:54:29,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-11-g13c0244, Compiled 2012/09/29 06:03:05 INFO 14:54:29,749 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:54:29,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 14:54:29,750 HelpFormatter - Program Args: -T UnifiedGenotyper -nt 6 -R /scratch/appli57_local_duplicates/reference/Homo_sapiens_assembly19.fasta -I /scratch/user/FILE.marked.realigned.fixed.recal.bam --dbsnp /scratch/appli57_local_duplicates/dbsnp/dbsnp_132.b37.vcf -L /scratch/appli57_local_duplicates/reference/exome_target_intervals.bed --metrics_file /scratch/user/FILE.snps.metrics -o /scratch/user/FILE.vcf INFO 14:54:29,750 HelpFormatter - Date/Time: 2013/03/20 14:54:29 INFO 14:54:29,750 HelpFormatter - --------------------------------------------------------------------------------- INFO 14:54:29,751 HelpFormatter - --------------------------------------------------------------------------------- INFO 14:54:29,783 ArgumentTypeDescriptor - Dynamically determined type of /scratch/appli57_local_duplicates/dbsnp/dbsnp_132.b37.vcf to be VCF INFO 14:54:29,799 GenomeAnalysisEngine - Strictness is SILENT INFO 14:54:29,906 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:54:29,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04 INFO 14:54:29,959 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/appli57_local_duplicates/dbsnp/dbsnp_132.b37.vcf WARN 14:54:30,190 VCFStandardHeaderLines$Standards - Repairing standard header line for field AF because -- count types disagree; header has UNBOUNDED but standard is A -- descriptions disagree; header has 'Allele Frequency' but standard is 'Allele Frequency, for each ALT allele, in the same order as listed' INFO 14:54:32,484 MicroScheduler - Running the GATK in parallel mode with 6 concurrent threads

And it does not move from there. In my destination folder, a bamschedule.*.tmp file appears every 5 minutes or so, and in top, the program seems to be running:

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
29468 valleem 19 0 20.6g 3.9g 10m S 111.5 4.2 28:45.46 java

Can you help me?


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