Running with gitlab-runner 13.8.0 (775dd39d)
  on scgn01-public-docker McK4j2hV
section_start:1614645800:prepare_executor
Preparing the "docker" executor
Using Docker executor with image fedora ...
Pulling docker image fedora ...
Using docker image sha256:33c4a622f37cfad474fd76ecd3e9c04e6434bd9a1668130537bd814ddbdce7a5 for fedora with digest fedora@sha256:3738909921e6d370a5c8dea69951b66af69264ba6b4bc270c856a682d11d5542 ...
section_end:1614645809:prepare_executor
section_start:1614645809:prepare_script
Preparing environment
Running on runner-mck4j2hv-project-190-concurrent-0 via scgn01.svi.edu.au...
section_end:1614645810:prepare_script
section_start:1614645810:get_sources
Getting source from Git repository
Fetching changes with git depth set to 50...
Reinitialized existing Git repository in /builds/biocellgen-public/sscocaller/.git/
Checking out 7370a797 as master...

Skipping Git submodules setup
section_end:1614645811:get_sources
section_start:1614645811:download_artifacts
Downloading artifacts
Downloading artifacts for buildStatic (17475)...
Downloading artifacts from coordinator... ok        id=17475 responseStatus=200 OK token=TYmx_a6A
section_end:1614645812:download_artifacts
section_start:1614645812:step_script
Executing "step_script" stage of the job script
$ ./src/sscocaller -h
Obtain allele counts for cell barcodes listed in barcodeFile at the SNP positions in VCF from the BAM file.

  Usage:
      sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix>

  Options:
      -t --threads <threads> number of BAM decompression threads [default: 4]
      -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
      -BQ --baseq <baseq>  base quality threshold for a base to be used for counting [default: 13]
      -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
      -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
      -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 10]
      -chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
      -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
      -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
      -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1]
      -h --help  show help

  Examples
      ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
section_end:1614645812:step_script
section_start:1614645812:cleanup_file_variables
Cleaning up file based variables
section_end:1614645813:cleanup_file_variables
Job succeeded