GSTAMA_COLLAPSE error - ref_allele = fasta_dict[scaffold][var_pos] IndexError: list index out of range

[jlandry69]

Description of the bug

Dear all,
Thank you for your work and the pipeline.
I am running your isoseq nf pipeline on PacBio reads.
I am getting an error during tama::collapse step.
I have attached the nexflow.log and a snapshot of the work directory containing the command and output files generated before crashing.
Thank you for your help on this and please let me know if you need more info.
Jonathan

Command used and terminal output

Nextflow command:
nextflow run nf-core/isoseq  \
    --input samplesheet_${RUNID}.csv \
    --primers primers.fa \
    --outdir isoseq_out_ultra \
    --fasta GRCh38.primary_assembly.genome.fa \
    --gtf gencode.v45.annotation.gtf \
    --entrypoint map \
    --aligner ultra \
    -profile standard

Error:
[...]
  ['transcript/4446740']
  Read mapping off scaffold
  chrM : -107
  ['transcript/4797600']
  Read mapping off scaffold
  chrM : -61
  ['transcript/4831734']
  Read mapping off scaffold
  chrM : -15
  ['transcript/4846452']
Command error:
  Traceback (most recent call last):
    File "/usr/local/bin/tama_collapse.py", line 6228, in <module>
      ref_allele = fasta_dict[scaffold][var_pos]
  IndexError: list index out of range

Relevant files

.nextflow.log
command.tar.gz

System information

Nextflow version: version 24.04.4
Hardware: HPC
Executor: slurm
Container engine: Apptainer
OS: Linux 5.15.0-124-generic
Version of nf-core/isoseq: v2.0.0