Analysis completed with empty caveman snps.ids vcf

[dawidsielski]

I am running CGPWGS on a large number of samples (around 800 pairs). In case of 27 the pipeline finished without an error, but caveman snps.ids.vcf.gz contains only a header.

Could you point me where could I search for the cause?

I was running it on an HPC cluster using singularity image, version 2.0.1 with this run params

export PCAP_THREADED_NO_SCRIPT=1
export PCAP_THREADED_FORCE_SYNC=1
export PCAP_THREADED_LOADBACKOFF=1
export PCAP_THREADED_REM_LOGS=1
PROTOCOL=WGS
OUTPUT_DIR='/var/spool/results'
REF_BASE='/var/spool/results/reference_files'
BAM_MT='/var/spool/data/CPCT02010267TII/CPCT02010267TII.bam'
IDX_MT='/var/spool/data/CPCT02010267TII/CPCT02010267TII.bam.bai'
BAM_WT='/var/spool/data/CPCT02010267R/CPCT02010267R.bam'
IDX_WT='/var/spool/data/CPCT02010267R/CPCT02010267R.bam.bai'
CONTIG_EXCLUDE='MT,NC_007605,hs37d5,GL%'
PINDEL_MAXCPU=8
SPECIES='human'
ASSEMBLY='GRCh37d5'
CAVESPLIT='800000'
SNVFLAG='/var/spool/results/flag.vcf.config.WGS.ini'
CPU=28
CLEAN_REF=1
SKIPBB=1
SKIPQC=1

These are five last lines from timing files that contained caveman in the name

==> WGS_CPCT02010267TII_vs_CPCT02010267R.time.CaVEMan <==
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

==> WGS_CPCT02010267TII_vs_CPCT02010267R.time.CaVEMan_annot <==
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

==> WGS_CPCT02010267TII_vs_CPCT02010267R.time.CaVEMan_setup <==
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

==> WGS_CPCT02010267TII_vs_CPCT02010267R.time.CaVEMan_split <==
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

==> WGS_CPCT02010267TII_vs_CPCT02010267R.time.cgpFlagCaVEMan <==
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

This is the content of the *time file in the work folder.

 Command being timed: "/opt/wtsi-cgp/bin/analysisWGS.sh /var/spool/results/run.params"
User time (seconds): 2200457.98
System time (seconds): 18570.81
Percent of CPU this job got: 2450%
Elapsed (wall clock) time (h:mm:ss or m:ss): 25:09:32
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 9836908
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 506
Minor (reclaiming a frame) page faults: 10819652688
Voluntary context switches: 105813361
Involuntary context switches: 80816834
Swaps: 0
File system inputs: 93244
File system outputs: 66220240
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0