AssertionError

[m-noonan]

Hello, I'm running IsoTools in command line and keep getting an AssertionError with the TALAM1 gene after sample import. Is this something on my end? Does it have to do with the annotation I'm using? I previously ran IsoTools with just 2 mouse samples and it worked just fine, so I'm not sure if it's something to do with my human genome/reference and/or samples. Any help would be appreciated!

samples='samples.txt'
anno='gencode.v43.annotation.gtf'
genome='GRCh38.primary_assembly.genome.fa'

run_isotools
--anno $anno
--log INFO
--progress_bar
--genome $genome
--samples $samples
--file_prefix ./isotools
--group_by group
--diff
--diff_plots 5
--diff NT/KD

59%|███████████████████████████████████████████████████▋ | 142870/243415 [1:21:17<57:12, 29.29genes/s]2023-06-15 19:14:41 ERROR: Gene TALAM1 chr11:65499311-65507432(-), 1 reference transcripts, 150 expressed transcripts TSS= {'hNT1': {65504026: 1}}, PAS={'hNT1': {65500537: 1}} -> TSS_unified= {'hNT1': {65500848: 1}}, PAS_unified={'hNT1': {65500537: 1}}
59%|███████████████████████████████████████████████████▋ | 142884/243415 [1:21:17<57:11, 29.30genes/s]
Traceback (most recent call last):
File "/home/data/Megan/anaconda3/bin/run_isotools", line 8, in
sys.exit(main())
File "/home/data/Megan/anaconda3/lib/python3.9/site-packages/isotools/run_isotools.py", line 66, in main
isoseq = load_isoseq(args)
File "/home/data/Megan/anaconda3/lib/python3.9/site-packages/isotools/run_isotools.py", line 155, in load_isoseq
isoseq.add_qc_metrics(args.genome, progress_bar=args.progress_bar)
File "/home/data/Megan/anaconda3/lib/python3.9/site-packages/isotools/_transcriptome_filter.py", line 68, in add_qc_metrics
g._unify_ends()
File "/home/data/Megan/anaconda3/lib/python3.9/site-packages/isotools/gene.py", line 897, in _unify_ends
assert end > tr['exons'][-1][0] or len(tr['exons']) == 1, 'error unifying %s: %s<=%s' % (tr["exons"], end, tr['exons'][-1][0])
AssertionError: error unifying [[65500537, 65500920], [65501008, 65504026]]: 65500848<=65501008

[MatthiasLienhard]

Hi m-nooan,

thank you for reporting this bug. I made an attempt to fix it, can you please download the development branch from git, install it and then run your analysis again?

git clone -b development https://github.com/MatthiasLienhard/isotools.git
cd isotools
python3 -m pip install .

If this does not work, would you be willing to share a small part of your data to reconstruct the bug on my side? I guess the easiest would be to extract all reads overlapping this gene with samtools.

Best, Matthias

[MatthiasLienhard]

This should be fixed now, in 0.3.4. If something is not working, please file a new issue.

[m-noonan]

Just wanted to come back and let you know I tried it with the update 0.3.4 and it worked! Thanks for the fix!