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DepthOfCoverage multiple samples

adri_somavillaadri_somavilla EdinburghMember
edited August 2016 in Ask the GATK team

Dear all,
I have about 300 bam files (whole-genome sequence) and I'm trying to get the DepthOfCoverage per chomosome.

I'm using a script to submit a job for each chromosome, like that:

java -jar /GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T DepthOfCoverage -R 'ref_gen.fa' -I samplesBam.list -L $Chr -o $Chr.DepthCov -nt 30 -omitIntervals -omitSampleSummary -omitLocusTable

The analysis started without problems, but after a while a got an error about "many files opened".
Sorry for not having the output, but I deleted before realise I was going to need them here.

Is there a better way to do that? I've tried sample by sample, but them I'll have 300x34 chromosomes files to get the average manually.
Thank you

Best Answer

Answers

  • adri_somavillaadri_somavilla EdinburghMember
    edited August 2016
  • adri_somavillaadri_somavilla EdinburghMember

    Thanks Sheila, I'll have a look!!

  • adri_somavillaadri_somavilla EdinburghMember

    @Sheila
    For information:
    I changed the 'open file' limit but it didn't work, so I'm running (version 3.5) without the -nt and -omitIntervals flags:

    java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R ref_gen -I samplesbam.list -L Chrom -o Chrom.DepthCov -omitSampleSummary -omitLocusTable

    It's working better than before, since it is writing the output now. Also, the estimated time isn't that bad for 263 WGS bam files:
    This is the smallest Chromosome, I'll see what happens to the largest one.

    INFO 11:46:02,855 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 11:46:02,855 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 11:46:02,856 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    INFO 11:46:32,861 ProgressMeter - CM000112.4:26185 16384.0 30.0 s 30.5 m 0.2% 4.5 h 4.5 h
    INFO 11:47:02,866 ProgressMeter - CM000112.4:59953 49152.0 60.0 s 20.3 m 0.4% 3.9 h 3.9 h
    INFO 11:47:32,872 ProgressMeter - CM000112.4:98221 81920.0 90.0 s 18.3 m 0.7% 3.6 h 3.6 h
    INFO 11:48:02,875 ProgressMeter - CM000112.4:131073 131072.0 120.0 s 15.3 m 0.9% 3.6 h 3.6 h
    INFO 11:48:32,879 ProgressMeter - CM000112.4:173241 163840.0 2.5 m 15.3 m 1.2% 3.4 h 3.4 h
    INFO 11:49:02,882 ProgressMeter - CM000112.4:212409 196608.0 3.0 m 15.3 m 1.5% 3.3 h 3.3 h
    INFO 11:49:32,886 ProgressMeter - CM000112.4:245861 245760.0 3.5 m 14.2 m 1.7% 3.3 h 3.3 h
    INFO 11:50:02,911 ProgressMeter - CM000112.4:289529 278528.0 4.0 m 14.4 m 2.1% 3.2 h 3.2 h
    INFO 11:50:32,914 ProgressMeter - CM000112.4:327597 311296.0 4.5 m 14.5 m 2.3% 3.2 h 3.2 h
    INFO 11:51:02,920 ProgressMeter - CM000112.4:363649 360448.0 5.0 m 13.9 m 2.6% 3.2 h 3.1 h
    INFO 11:51:32,927 ProgressMeter - CM000112.4:400517 393216.0 5.5 m 14.0 m 2.8% 3.2 h 3.1 h

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