chapmanb/bcbb — Issue #45: Test test_3_empty_fastq not passing with GATK 1.3
Author: vals
Created: 2011-11-16 10:43:04+00:00
State: open

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

```bash
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

```bash
##### 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](http://www.broadinstitute.org/gsa/wiki/index.php/GATK_release_1.3):

> * We now throw an exception when there is no data instead of creating an empty csv file.