Unsupported Operand Error

[jainronit]

Hi, I've encountered an error regarding an unsupported operand while running shapemapper2 on my samples. Do you know what the issue here might be?

ERROR: Component "RenderFigures" (RNA:ZNF318_chr6_43369415:37-166) failed, giving the following error message:
Traceback (most recent call last):
File "/oak/stanford/groups/nicolemm/ronitj/shapemapper2-2.3/internals/python/pyshapemap/../../bin/render_figures.py", line 2133, in
qc_pass = qc_stats(masked_sequence,
File "/oak/stanford/groups/nicolemm/ronitj/shapemapper2-2.3/internals/python/pyshapemap/../../bin/render_figures.py", line 233, in qc_stats
diff = rx_rate-bg_rate
TypeError: unsupported operand type(s) for -: 'NoneType' and 'float'

[jainronit]

Hi @Psirving, just wanted to follow up on this - would appreciate any guidance on this!

[Psirving]

Hi, I haven't seen this before. Can you attach your "_profile.txt" file?

[jainronit]

Yes, here it is:

dedup_NoPUS1_noadapters_nofilters_ZNF318_chr6_43369415_37-166_profile.txt

[Psirving]

Everything in this file is 0 or NaN, which would cause the issue above. Likely 0 reads in the input fastqs align to the target sequence. It could be those files are empty, or they are the wrong sequencing samples, or the target sequence or primer locations are wrong. The prefix in this file name suggests that there are some pre-processing steps done to the fastqs before running ShapeMapper, check that those worked correctly.

I can dig deeper if you think this is a ShapeMapper issue.