AssemblyEvidenceSource Category Number Mismatch Error

[DarioS]

I am doing the three stages separately. It has worked smoothly in the past. When I run the calling stage, I get an error about the number of categories mismatching.

Wed Sep 23 16:30:06 AEST 2020: Skipping assembly        /scratch/hm82/OSCC//assembled/PONassembly.bam
Wed Sep 23 16:30:06 AEST 2020: Start calling    /scratch/hm82/OSCC//structuralVariants/HeadNeckAllHealthy.vcf.gz
Wed Sep 23 16:30:06 AEST 2020: Running  IdentifyVariants        /scratch/hm82/OSCC//structuralVariants/HeadNeckAllHealthy.vcf.gz
   ...           ...
ERROR   2020-09-23 16:30:14     AssemblyEvidenceSource  Fatal error: GRIDSS assembly does not have the expected number of input categories (found 1, expected 10). GRIDSS performs joint assembly and does not support per-input assembly. Make sure the same input and labels are specified in the same order for the assembly and variant calling steps.

But, there are indeed 10 categories in the resulting file of the second stage, the assemble stage.

@PG     ID:gridss0      PN:gridss       VN:2.9.4-gridss
@PG     ID:samtools     PN:samtools     PP:gridss0      VN:1.10 CL:samtools view -H /scratch/hm82/OSCC/assembled/PONassembly.bam
@CO     gridss_input_category=Oral_1-N
@CO     gridss_input_category=Oral_2-N
@CO     gridss_input_category=Oral_3-N
@CO     gridss_input_category=Oral_4-N
@CO     gridss_input_category=Oral_5-N
@CO     gridss_input_category=Oral_6-N
@CO     gridss_input_category=Oral_7-N
@CO     gridss_input_category=Oral_8-N
@CO     gridss_input_category=Oral_9-N
@CO     gridss_input_category=Oral_10-N

What could be triggering this error?

[d-cameron]

Duplicate of #354 (see this issue for the workaround)/#403

Actioning as #397

[d-cameron]

It has worked smoothly in the past.

If you were running a version of GRIDSS before I put this sanity check in, then it would have silently misattributed assembly support to the wrong sample.