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Psy-Fer / SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data
MIT License
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Fast5_fetcher_multi.py no output #55

Open Salvobioinfo opened 2 years ago

Salvobioinfo commented 2 years ago

Hello, I tried fast5_fetcher using follow cmd: python3.6 fast5_fetcher_multi.py -p File.paf.gz -i /name.index --seq_sum sequencing_summary.txt.gz -o ./fast5_fetcher but the only output i got is the error message: no filenames list built, check inputs I checked my input files and apparently they look ok. What could I be doing wrong? Thank you in advance.

Salvobioinfo commented 2 years ago

I found an issue in the summary file. It was malformed, indeed the first column was named “filename_fastq” and not “filename_fast5”. So, the function “get_filenames” did not work.

Psy-Fer commented 2 years ago

Hey, Yea a bit of work needs to be done since they modified and have multiple versions of, the summary files now.

I can do a quick edit for this when I'm at work tomorrow and I'll let you know when the code is pushed.

James