Master_vcf terminated for single-sample run

[mh-tan]

When running only one sample, it terminated at the Master_vcf step. Upon checking .command.err, it shows find: '*.gvcf': No such file or directory. Further inspecting the process folder, it looks like the single VCF file is linked as a .raw.gvcf without an ID prefix.

ARDaP ran successfully for >1 samples.

executor >  local (14)
[d7/25a5f6] process > IndexReference                      [100%] 1 of 1 ✔
[3c/456b6b] process > Trimmomatic (SampleID1)        [100%] 1 of 1 ✔
[2d/719e34] process > Downsample (SampleID1)         [100%] 1 of 1 ✔
[c0/e33f74] process > ReferenceAlignment (SampleID1) [100%] 1 of 1 ✔
[4c/46d8ef] process > Deduplicate (SampleID1)        [100%] 1 of 1 ✔
[85/61bdd2] process > VariantCalling (SampleID1)     [100%] 1 of 1 ✔
[25/ebde2e] process > SqlSnpsIndels (SampleID1)      [100%] 1 of 1 ✔
[51/ca4c4a] process > R_report (SampleID1)           [100%] 1 of 1 ✔
[13/8a5f60] process > VariantCallingGVCF (SampleID1) [100%] 1 of 1 ✔
[56/381cd9] process > Master_vcf                          [100%] 5 of 5, failed: 5, retries: 4 ✘
[-        ] process > snp_matrix                          -
[b2/ffc3b4] NOTE: Process `Master_vcf` terminated with an error exit status (2) -- Execution is retried (1)
[81/1337cf] NOTE: Process `Master_vcf` terminated with an error exit status (2) -- Execution is retried (2)
[6f/e6fd8a] NOTE: Process `Master_vcf` terminated with an error exit status (2) -- Execution is retried (3)
[92/09b4f2] NOTE: Process `Master_vcf` terminated with an error exit status (2) -- Execution is retried (4)
Error executing process > 'Master_vcf'

Caused by:
  Process `Master_vcf` terminated with an error exit status (2)

Command executed:

  bash Master_vcf.sh k96243
  gatk VariantFiltration -R k96243.fasta -O out.filtered.vcf -V out.vcf     --cluster-size 3 -window 10     -filter "QD < 10.0" --filter-name "QDFilter"     -filter "MQ < 30.0" --filter-name "MQFilter"     -filter "FS > 60.0" --filter-name "HaplotypeScoreFilter"

Command exit status:
  2

[esteinig]

@dsarov Mun/Torsten did some great sleuthing/debugging of this - edge case but important for single isolate runs

@mh-tan I believe you were able to fix it - if so could you open a pull request with the changes? :)

[dsarov]

@mh-tan @esteinig Let me know if this is still an issue and I can patch it. Shouldn't be too tough - I've just never run a single sample! The master vcf and snp matrix steps can probably be completely ignored for a single sample anyway because those steps are primarily for phylogenetic comparisons.

[mh-tan]

@dsarov I've created a pull request with the fix. Let me know if you don't see it. Cheers.