IndexError: list index out of range

[NikoHensley]

Hello, I apologize for the novice question but I am trying to run TAMA Collapse and then TAMA Merge on isoseq data that has been mapped to a genome, once using minimap2 and once using uLTRA with a previous annotation as guide. My goal to to use the isoseq data to update gene models for an improved annotation.

However, when I try to run TAMA Collapse on my sorted alignments from either uLTRA or minimap2, I get the following error:

Traceback (most recent call last):
  File "/local/workdir/Hensley/genome_finalize/annotation/tama_merge_collapse/tama/tama_collapse.py", line 5136, in <module>
    sam_flag = int(line_split[1])
IndexError: list index out of range

I tried re-downloading the program and using the test data in the test files and it actually produces the same error at the same line. I am unsure if I'm not correctly entering the required calls or something different, as I find it odd that even the test data wouldn't run correctly. Any help would be appreciated!

My code: python /local/workdir/Hensley/genome_finalize/annotation/tama_merge_collapse/tama/tama_collapse.py -s /local/workdir/Hensley/genome_finalize/annotation/tama_merge_collapse/tama/test_files/test_genome.fa -f /local/workdir/Hensley/genome_finalize/annotation/tama_merge_collapse/tama/test_files/gmap_test.sam -p test_out

Using: Python 2.7.18

[jlandry69]

Hi, was just wondering if there is some update on this issue. I am getting a very similar error. Thanks