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EichlerLab / smrtsv2

Structural variant caller
MIT License
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Temp file not found when genotyping #32

Closed RSherman15 closed 5 years ago

RSherman15 commented 5 years ago

I am getting the following error in the genotyping step. I tried rerunning in case it was a fluke with the temp file, but I got the same error both times (with different temp file names).

[Wed Apr 24 12:04:31 2019]
rule gt_map_sample_reads:
    input: /work-zfs/mschatz1/rsherman/giab/HG002_Illumina_bam/CT21796_NA24385_NIST_UDI22_HiseqX_19122017_Proband_S1.bam, altref/ref.fasta, altref/ref.fasta.bwt, altref/ref.fasta.alt, altref/alt_info.bed, altref/map_regions.bed
    output: samples/hg002/alignments.cram, samples/hg002/alignments.cram.crai
    log: samples/hg002/alignments.log
    jobid: 0
    wildcards: sample=hg002

[Wed Apr 24 12:04:31 2019]
Error in rule gt_map_sample_reads:
    jobid: 0
    output: samples/hg002/alignments.cram, samples/hg002/alignments.cram.crai
    log: samples/hg002/alignments.log

RuleException:
FileNotFoundError in line 437 of /home-net/home-4/rsherma8@jhu.edu/bin/packages/smrtsv2/rules/genotype.snakefile:
[Errno 2] No such file or directory: '/scratch/groups/ssalzbe1/rsherman/lustre_temp/map_sample_hg002_oztt_ff_'
  File "/home-net/home-4/rsherma8@jhu.edu/bin/packages/smrtsv2/rules/genotype.snakefile", line 437, in __rule_gt_map_sample_reads
  File "/home-net/home-4/rsherma8@jhu.edu/bin/packages/smrtsv2/dep/conda/build/envs/python3/lib/python3.6/tempfile.py", line 368, in mkdtemp
  File "/home-net/home-4/rsherma8@jhu.edu/bin/packages/smrtsv2/dep/conda/build/envs/python3/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
RSherman15 commented 5 years ago

I think this was an issue on my end - another program had deleted the whole temp directory so [path]/lustre_temp did not exist rather than the file not existing.