Sequence corrector error

[jodyphelan]

The pipeline is exiting with the following error:

/mnt/storage8/jody/software/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py:245: RuntimeWarning: divide by zero encountered in long_scalars
  freq = variant.count / d
Traceback (most recent call last):
  File "/mnt/storage8/jody/software/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py", line 433, in <module>
    merged_variants)
  File "/mnt/storage8/jody/software/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py", line 328, in correct_sequence
    raise RuntimeError(s)
RuntimeError: Error: Unable to determine variant sequence. Conflicting (overlapping) variant sequences present.

Is there something wrong with the command I am using?

shapemapper --name example --target ~/ref.fa --out test --correct-seq --folder minus --modified --folder pos --untreated --folder minus --denatured --folder denatured --nproc 60 --star-aligner

[Psirving]

Sorry for not replying sooner. Your command looks correct. The error Conflicting (overlapping) variant sequences present. indicates that there may be multiple sequence variants in the untreated sample, and ShapeMapper could not find a unique corrected sequence. Were you able to resolve this?

[jodyphelan]

Hi @Psirving, the reference I was using was quite divergent from the sample and I was able to resolve this by using a closer reference. Thanks!