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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Issue in Quality Control #260

Open luishdez35 opened 2 years ago

luishdez35 commented 2 years ago

Hello, I have one issue running the quality control part for the tutorial.

for i in *; do phyluce_assembly_get_fastq_lengths --input $i/split-adapter-quality-trimmed/ --csv; done

For every sample (species) i has the same error

Traceback (most recent call last): File "/Users/luiscarloshernandez/opt/anaconda3/envs/phyluce-2/bin/phyluce_assembly_get_fastq_lengths", line 106, in main() File "/Users/luiscarloshernandez/opt/anaconda3/envs/phyluce-2/bin/phyluce_assembly_get_fastq_lengths", line 68, in main lengths = numpy.array(lengths) UnboundLocalError: local variable 'lengths' referenced before assignment

I read in other issue post that I need to modify the code for phyluce_assembly_get_fastq_lengths, but I don't know how do that, I hope you can help me. Thanks a lot

brantfaircloth commented 2 years ago

Yes, I am not sure I have fixed this issue... you can safely skip this step.

luishdez35 commented 2 years ago

Thanks for the quick answer, yes I skip this step, buy actually I need the stats, do you think FastQC work? Or do you known other option,

Thanks a lot!!