Unexpected alignment name collision

[graceooh]

There seems to be an error in call-sSV regarding "Unexpected alignment name collision". I wonder if this has to do with uclahs-cds/pipeline-call-gSNP#79 as similar error messages (see additional context).

• Pipeline release version: v5.3.1
• Cluster you are using: Slurm
• Node type: F72
• Submission method: submission script
• Actual submission script:
  python3 /hot/software/package/tool-submit-nf/Python/release/2.5.1/submit_nextflow_pipeline.py
  --nextflow_script /hot/user/jieunoh/metapipeline-DNA/main.nf
  --nextflow_config /hot/user/jieunoh/su2c/metapipeline-DNA/test_ancestry_align_dna_batch_29/test_ancestry.config
  --pipeline_run_name batch_29_metapipeline
  --email jieunoh@mednet.ucla.edu
  --partition_type F2
  --nextflow_yaml /hot/user/jieunoh/su2c/metapipeline-DNA/test_ancestry_align_dna_batch_29/batch_29_dna_metapipeline.yaml `
• Sbatch or qsub command and logs if applicable
• Config files:
• /hot/user/jieunoh/su2c/metapipeline-DNA/test_ancestry_align_dna_batch_29/test_ancestry.config
• Path to the working directory
• Any logs produced by the pipeline:
• Main metapipeline log: * /hot/user/jieunoh/su2c/metapipeline-DNA/test_ancestry_align_dna_batch_29/batch_29_metapipeline.log
• Sample 1 log: /hot/user/jieunoh/su2c/output/workdir/batch_29/1c/bed05fc5234158806688c6e55226ee/.command.log
• Sample 2 log: /hot/user/jieunoh/su2c/output/workdir/batch_29/5f/05d760c814eab08f5a32b2c6c69e7e/.command.log
• Sample 3 log: /hot/user/jieunoh/su2c/output/workdir/batch_29/eb/a68f46f6a746624d7ebfc1ce92ca79/.command.log

Additional context
The error message is similar to uclahs-cds/pipeline-call-gSNP#79

[2024-02-29T03:28:09.957862Z] [5007b20e776c] [89_1] [WorkflowRunner] [ERROR] [2024-02-29T03:27:59.960427Z] [5007b20e776c] [89_1] [generateCandidateSV_0000] std::exception::what: Unexpected alignment name collision. Source: 'BWA-MEM2-2.2.1_GATK-4.2.4.1_SU2C_DTB-143-T.bam' [2024-02-29T03:28:09.957862Z] [5007b20e776c] [89_1] [WorkflowRunner] [ERROR] [2024-02-29T03:27:59.963260Z] [5007b20e776c] [89_1] [generateCandidateSV_0000] Existing read: 920:308:HG7MHCCXY:6:2122:7933:31652/2 chrom:pos:strand chr6:32699476:- cigar: 150M templateSize: -397 SA: chr6_GL000256v2_alt,4100134,-,150M,21,1; mateChrom:pos:strand chr6:32699229:+ [2024-02-29T03:28:09.957862Z] [5007b20e776c] [89_1] [WorkflowRunner] [ERROR] [2024-02-29T03:27:59.966097Z] [5007b20e776c] [89_1] [generateCandidateSV_0000] New read: 920:308:HG7MHCCXY:6:2122:7933:31652/2 chrom:pos:strand chr6:32699476:- cigar: 150M templateSize: -394 SA: chr6_GL000256v2_alt,4100134,-,150M,21,1; mateChrom:pos:strand chr6:32699232:+