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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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Test test_3_empty_fastq not passing with GATK 1.3 #45

Closed vals closed 12 years ago

vals commented 12 years ago

Hey Brad, I saw you had made a commit for GATK 1.3 compatibility, so I installed it and tried to run the tests. Unfortunately the test test_3_empty_fastq gets stuck on a call to GATK. Specifically

java -Xmx6g -Djava.io.tmpdir=/bubo/home/h10/vale/bcbb/nextgen/tests/tmp/tmppV8I7Y -jar /bubo/home/h10/vale/opt/GenomeAnalysisTK-1.3-14-g348f2db/GenomeAnalysisTK.jar -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile /bubo/home/h10/vale/bcbb/nextgen/tests/tx/1_110221_FC_withspace_8-sort-dup.recal -I /bubo/home/h10/vale/bcbb/nextgen/tests/1_110221_FC_withspace_8-sort-dup.bam -R /bubo/home/h10/vale/bcbb/nextgen/tests/data/automated/tool-data/../../genomes/hg19/seq/hg19.fa -l INFO -U -OQ --default_platform illumina --knownSites /bubo/home/h10/vale/bcbb/nextgen/tests/data/automated/tool-data/../../genomes/hg19/variation/dbsnp_132.vcf --phone_home NO_ET -nt 5

will give the error

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db): 
##### 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 Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Bad input: Could not find any usable data in the input BAM file(s).
##### ERROR ------------------------------------------------------------------------------------------

The test passes when using GATK 1.2, I think this is due to this point in the changelog:

  • We now throw an exception when there is no data instead of creating an empty csv file.
chapmanb commented 12 years ago

Valentine; Thanks for reporting this. I just pushed fixes that will check for empty files and avoid this issue. Let me know if you run into any other problems.