call_gCNV_Delly; Please increase the window size. Coverage is too low!

[rhughwhite]

• Full error below. Low coverage error may relate to sample being WXS i.e. genomics windows with low/no coverage.
• Initially running as part of metapipeline-DNA, but also re-run with 1) call-gSNP -> call-gSV individually 2) align-DNA -> call-gSV, which produce the same error
• F72
• call-gSV v4.0.1
• Python submission script used - /hot/data/unregistered/Robinson-Livingstone-PRAD-IGXR/exome/metapipeline-DNA/troubleshooting/call-gSV/run_call-gSV.sh
• log = /hot/data/unregistered/Robinson-Livingstone-PRAD-IGXR/exome/metapipeline-DNA/troubleshooting/call-gSV/RLPRIGXR000005_sorted_bed.log
• config = hot/data/unregistered/Robinson-Livingstone-PRAD-IGXR/exome/metapipeline-DNA/troubleshooting/call-gSV/config/RLPRIGXR000005.config

Error executing process > 'call_gCNV_Delly (1)'

Caused by: Process call_gCNV_Delly (1) terminated with an error exit status (1)

Command executed:

set -euo pipefail delly cnv --genome Homo_sapiens_assembly38.fasta --outfile DELLY-1.1.3_CNV_RLPRIGXR_RLPRIGXR000005-N001-B01-F.bcf --svfile DELLY-1.1.3_SV_RLPRIGXR_RLPRIGXR000005-N001-B01-F.bcf --mappability Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz RLPRIGXR000005-N001-B01-F_realigned_recalibrated_merged_dedup.bam

Command exit status: 1

Command output: (empty)

Command error: [2023-Jan-26 18:35:24] delly cnv --genome Homo_sapiens_assembly38.fasta --outfile DELLY-1.1.3_CNV_RLPRIGXR_RLPRIGXR000005-N001-B01-F.bcf --svfile DELLY-1.1.3_SV_RLPRIGXR_RLPRIGXR000005-N001-B01-F.bcf --mappability Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz RLPRIGXR000005-N001-B01-F_realigned_recalibrated_merged_dedup.bam [2023-Jan-26 18:35:45] Scanning Windows Please increase the window size. Coverage is too low!

Work dir: /scratch/27/e641c20a0b9e0e43814a01843549a7

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

[rhughwhite]

Update: Paul pointed out that results from call-gSV are likely not that useful for WXS, so this issue is lower priority/unsure if the pipeline needs to be able to handle WXS?

[tyamaguchi-ucla]

For CNV, Delly should be able to work with WXS but we'll have to update the module to accept the -b option to input the target region. Let us know if you are interested in looking into CNV soon. Otherwise we can make this issue low priority. For SV, the developer doesn't recommend using Delly for WXS. (designed for WGS)

See https://github.com/dellytools/delly/issues/275

[rhughwhite]

Yeah this is lower priority.

we'll have to update the module to accept the -b option to input the target region. Let us know if you are interested in looking into CNV soon.

Would this also apply to call-sSV?

[tyamaguchi-ucla]

Would this also apply to call-sSV?

call-sSV now has Manta, which works with WXS - https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md