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Decompress with dsub

This example demonstrates how to decompress files stored in a Google Cloud Storage bucket by submitting a simple command from a shell prompt on your laptop. The job executes in the cloud. As input, we start with a single compressed variant call format (VCF) file from the 1000 Genomes Project.

We then proceed to an example that demonstrates processing multiple files, using a small list of VCFs. All of the source VCF files are stored in a public bucket at gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/:

  • 20130723_phase3_wg/cornell/ALL.ChrY.Cornell.20130502.SNPs.Genotypes.vcf.gz
  • 20140708_previous_phase3/v2_vcfs/ALL.chr21.phase3_shapeit2_mvncall_integrated_v2.20130502.genotypes.vcf.gz
  • 20140708_previous_phase3/v1_vcfs/ALL.chr21.phase3_shapeit2_mvncall_integrated.20130502.genotype.vcf.gz
  • 20110721_exome_call_sets/bcm/ALL.BCM_Illumina_Mosaik_ontarget_plus50bp_822.20110521.snp.exome.genotypes.vcf.gz

Setup

Decompress one file

Submit the job

The following command will submit a job to decompress the first input file from the list above and write the decompressed file to a Cloud Storage bucket you have write access to.

To run a command to decompress the VCF file, type:

dsub \
  --provider google-cls-v2 \
  --project MY-PROJECT \
  --zones "us-central1-*" \
  --logging "gs://MY-BUCKET/decompress_one/logging" \
  --disk-size 200 \
  --image ubuntu:14.04 \
  --input INPUT_VCF="gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20130723_phase3_wg/cornell/ALL.ChrY.Cornell.20130502.SNPs.Genotypes.vcf.gz" \
  --output OUTPUT_VCF="gs://MY-BUCKET/decompress_one/output/ALL.ChrY.Cornell.20130502.SNPs.Genotypes.vcf" \
  --command 'gunzip ${INPUT_VCF} && \
             mv ${INPUT_VCF%.gz} $(dirname ${OUTPUT_VCF})' \
  --wait

Set MY-PROJECT to your cloud project name, and set MY-BUCKET to a cloud bucket on which you have write privileges.

You should see output like:

Job: gunzip--<userid>--170224-114336-37
Launched job-id: gunzip--<userid>--170224-114336-37
        user-id: <userid>
Waiting for jobs to complete...

Because the --wait flag was set, dsub will block until the job completes.

Check the results

To list the output, use the command:

gsutil ls gs://MY-BUCKET/decompress_one/output

Output should look like:

gs://MY-BUCKET/decompress_one/output/ALL.ChrY.Cornell.20130502.SNPs.Genotypes.vcf

To see the first few lines of the decompressed file, run:

gsutil cat gs://MY-BUCKET/decompress_one/output/*.vcf | head -n 5

Output should look like:

##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=PASS,Description="Passing basic quality fiters">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

Decompress multiple files

dsub allows you to define a batch of tasks to submit together using a tab-separated values (TSV) file listing the inputs and outputs. Each line lists the inputs and outputs for a separate task.

More on dsub batch jobs can be found in the README.

Create a TSV file

Open an editor and create a file submit_list.tsv:

--input INPUT_VCF	--output OUTPUT_VCF
gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20140708_previous_phase3/v2_vcfs/ALL.chr21.phase3_shapeit2_mvncall_integrated_v2.20130502.genotypes.vcf.gz	gs://MY-BUCKET/decompress_list/output/*.vcf
gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20140708_previous_phase3/v1_vcfs/ALL.chr21.phase3_shapeit2_mvncall_integrated.20130502.genotype.vcf.gz	gs://MY-BUCKET/decompress_list/output/*.vcf
gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20110721_exome_call_sets/bcm/ALL.BCM_Illumina_Mosaik_ontarget_plus50bp_822.20110521.snp.exome.genotypes.vcf.gz	gs://MY-BUCKET/decompress_list/output/*.vcf

The first line of the file lists the input and output parameter names. Each subsequent line lists the parameter values. Replace MY-BUCKET with a Cloud bucket on which you have write privileges.

Note that for the output parameter, for simplicity, we used wildcards to match the 1 VCF file each task outputs instead of explicitly listing the complete output file name.

Submit the job

dsub \
  --provider google-cls-v2 \
  --project MY-PROJECT \
  --zones "us-central1-*" \
  --logging "gs://MY-BUCKET/decompress_list/logging" \
  --disk-size 200 \
  --image ubuntu:14.04 \
  --command 'gunzip ${INPUT_VCF} && \
             mv ${INPUT_VCF%.gz} $(dirname ${OUTPUT_VCF})' \
  --tasks submit_list.tsv \
  --wait

Output should look like:

Job: gunzip--<userid>--170224-122223-54
Launched job-id: gunzip--<userid>--170224-122223-54
        user-id: <userid>
  Task: task-1
  Task: task-2
  Task: task-3
Waiting for jobs to complete...

when all tasks for the job have completed, dsub will exit.

Check the results

To list the output objects, use the command:

gsutil ls gs://MY-BUCKET/decompress_list/output

Output should look like:

gs://MY-BUCKET/decompress_list/output/ALL.BCM_Illumina_Mosaik_ontarget_plus50bp_822.20110521.snp.exome.genotypes.vcf
gs://MY-BUCKET/decompress_list/output/ALL.ChrY.Cornell.20130502.SNPs.Genotypes.vcf
gs://MY-BUCKET/decompress_list/output/ALL.chr21.phase3_shapeit2_mvncall_integrated.20130502.genotype.vcf
gs://MY-BUCKET/decompress_list/output/ALL.chr21.phase3_shapeit2_mvncall_integrated_v2.20130502.genotypes.vcf