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

[jlandry69]

Dear all,
Thank you for your work and the pipeline.
I am running the isoseq nextflow pipeline on PacBio reads (I have posted the same error on thei Github page as well here)

I am getting an error during tama::collapse step.

I have being rerunning the job independently of the nextflow framework and below is the command

tama_collapse.py \ -s NT3SR3Lib.chunk.2.bam \ -f GRCh38.primary_assembly.genome.fa \ -p NT3SR3Lib.chunk.2 \ -x no_cap -b BAM -a 100 -m 10 -z 100

and the error produced:

[...]
['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']
Traceback (most recent call last):
File "/flash/home/landryjo/conda-envs/tama/bin/tama_collapse.py", line 6228, in
ref_allele = fasta_dict[scaffold][var_pos]
IndexError: list index out of range

The complete log can be found here:
error.log.gz

Thank you for your help on this and please let me know if you need more info.
Jonathan