IndexError: list index out of range

[antoine4ucsd]

Hello
I am using quasitools to generate consensus an specify the minimum frequency of 20% required for a base to be incorporated into the mixed base consensus sequence
It works for some of my samples but for others, I have this error:

quasitools consensus -p 20 -o  myouput input.bam  reference.fasta

Traceback (most recent call last):
  File "/Users/antoinechaillon/opt/miniconda3/bin/quasitools", line 10, in <module>
    sys.exit(cli())
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/decorators.py", line 84, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/quasitools/commands/cmd_consensus.py", line 52, in cli
    conseq = mrc.to_consensus(percentage)
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/quasitools/mapped_read.py", line 159, in to_consensus
    pileup = self.pileup(indels=(percentage == 100))
  File "/Users/antoinechaillon/opt/miniconda3/lib/python3.9/site-packages/quasitools/mapped_read.py", line 100, in pileup
    pileup[i].get(self.reference.sub_seq(i, i).upper(), 0)\
IndexError: list index out of range

I was able to get full genome consensus with other algorithm (e.g. cliqueSNV)
any advice or parameters I can adapt?

thank you

[ericenns]

Hi @antoine4ucsd,
This error usually occurs when the alignment does not meet the minimum required coverage. This is hardcoded to 100 bases (https://github.com/phac-nml/quasitools/blob/master/quasitools/mapped_read.py#L166). Unfortunately this is not user configurable at the moment.

[antoine4ucsd]

thank you