Shorah: UnboundLocalError: local variable 'end' referenced before assignment

[ptapiaisp]

Hi, I am running shorah (installed with conda) and I am getting an error, my command line is:

shorah shotgun -b my_bam.bam -f CoV.fasta -a 0.1 -w 201 -x 100000 -c 10 -r CoV:1-29903

Error is:
Traceback (most recent call last):
File "/miniconda3/bin/shorah", line 14, in
main()
File "/miniconda3/lib/python3.7/site-packages/shorah/cli.py", line 196, in main
args.func(args)
File "/miniconda3/lib/python3.7/site-packages/shorah/cli.py", line 75, in shotgun_run
shotgun.main(args)
File "/miniconda3/lib/python3.7/site-packages/shorah/shotgun.py", line 452, in main
runlist = win_to_run(alpha, seed)
File "/miniconda3/lib/python3.7/site-packages/shorah/shotgun.py", line 336, in win_to_run
del end
UnboundLocalError: local variable 'end' referenced before assignment

any idea?

[DrYak]

Hum, this is intriguing: I haven't met this error message before. Looks like ShoRAH has trouble parsing back the windows files it has generated -- the coverage.txt file seems empty, something might have gone wrong when dividing the alignment BAM into overlapping windows.

Could you please provide your CoV.fasta and my_ba.bam files, so I can try replicating the problem and investigate ?

Or at least could you provide the content of the files shorah.log and coverage.txt that were producing when running ShoRAH, so we investigate what has happened ?

(Alternatively, you can also have a look at the V-pipe pipeline, that we also use to investigate SARS-CoV-2. Internally it also uses ShoRAH2 for SNV calling and local per-window haplotype reconstruction, but might be a bit easier to use, see this tutorial )