ReduceReads terminated before finishing and produce 0 size output
Posted in Ask the team | Last updated on 2013-10-15 17:12:00


Comments (10)

I'm using GATK 2.74 on my server with Java 1.7 on Mac. I'm running through many .bam files that was produced by the upstream PrintReads. I am using a for-loop in a shell script to loop all the .bam files through ReduceReads Some of these bam files were not compressed by GATK-ReduceReads, and it gives 0B .bam output files.

The command line I use is following:

java -Xmx10g -Djava.awt.headless=true -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T ReduceReads \ -R ./GATK_ref/hg19.fasta \ -S LENIENT \ -log ../GATK/BQSR/log/file1.compress.log \ -I ../GATK/BQSR/file1.recal.bam \ -o ../GATK/BQSR/file1.compressed.bam

I'm copying the tail part of the log for one of the failed .bam files: from this log, I don't see any error. Maybe ReduceReads walker just terminated itself earlier???

INFO 10:28:13,654 ProgressMeter - chr4:48710213 2.47e+07 19.2 m 46.0 s 23.6% 81.4 m 62.2 m INFO 10:28:43,657 ProgressMeter - chr4:83322785 2.54e+07 19.7 m 46.0 s 24.7% 79.8 m 60.1 m INFO 10:29:13,659 ProgressMeter - chr4:112743605 2.60e+07 20.2 m 46.0 s 25.6% 78.8 m 58.6 m INFO 10:29:43,662 ProgressMeter - chr4:151294343 2.67e+07 20.7 m 46.0 s 26.8% 77.1 m 56.4 m INFO 10:30:13,664 ProgressMeter - chr4:184999795 2.72e+07 21.2 m 46.0 s 27.9% 75.9 m 54.7 m INFO 10:30:43,667 ProgressMeter - chr5:14341390 2.79e+07 21.7 m 46.0 s 28.6% 75.9 m 54.2 m INFO 10:31:13,796 ProgressMeter - chr5:37088471 2.85e+07 22.2 m 46.0 s 29.3% 75.7 m 53.6 m INFO 10:31:43,798 ProgressMeter - chr5:67907077 2.92e+07 22.7 m 46.0 s 30.3% 74.9 m 52.3 m INFO 10:32:13,914 ProgressMeter - chr5:90107126 2.97e+07 23.2 m 46.0 s 31.0% 74.8 m 51.7 m INFO 10:32:44,969 ProgressMeter - chr5:127450350 3.03e+07 23.7 m 46.0 s 32.2% 73.7 m 50.0 m


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