Sailfish error: gzip broken pipe

[olgabot]

A couple things are happening wrong here.

1. Sailfish is being run with only ONE of the read-pairs, R1 for paired-end reads! It should be run on both at once!! I'm very concerned that other pipelines have been run with this because the output gene expression counts are on only half of the reads
2. Sailfish exits with return code 11, a segmentation fault. This may be because of an error in argument order, so I'll check this out.

{'index': 'none', 'num_processors': 16, 'do_not_submit': True, 'out_dir': '/home/obotvinnik/projects/singlecell_pnms/analysis/singlecell_pnms_pe_v1/M3_09_R1.sailfish', 'read1': '/home/obotvinnik/projects/singlecell_pnms/data/M3_09_R1.fastq.gz', 'read2': None, 'out_sh': 'M3_09_R1.sailfish.sh', 'job_name': 'M3_09_R1.sailfish.sh'}
Version Info: This is the most recent version

Library format { type:single end, relative orientation:none, strandedness:unstranded }
reading index . . . Sailfish terminated with return code 11
sailfish: /home/robp/Sailfish-0.6.3-Source/src/QuantificationDriver.cpp:152: int runKmerCounter(const string&, uint32_t, const string&, const std::vector<ReadLibrary>&, const string&, bool): Assertion `status == 0' failed.

gzip: bash: line 1: 21303 Aborted                 sailfish quant --index none -l "T=SE:S=U" -r <(gunzip -c /home/obotvinnik/projects/singlecell_pnms/data/M3_09_R1.fastq.gz) --out /home/obotvinnik/projects/singlecell_pnms/analysis/singlecell_pnms_pe_v1/M3_09_R1.sailfish --threads 16
stdout: Broken pipe
Nodes:        tscc-1-48
discarding /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/olga/bin to PATH

[olgabot]

The error seems to be happening because the index isn't getting specified. I can't seem to find where SailfishGenomeIndexLocation is defined

[olgabot]

nvm, found it in public/scala/src/org/broadinstitute/sting/queue/util/YeowareUtils.scala

[olgabot]

Gah, turns out it's because I didn't have the GENOME environment set. Why is this required? And why isn't there a backup option, or an error message specifying that you don't have this set?