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Fast5_fetcher_multi.py no output #55

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Salvobioinfo opened this issue Apr 2, 2022 · 2 comments
Open

Fast5_fetcher_multi.py no output #55

Salvobioinfo opened this issue Apr 2, 2022 · 2 comments

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@Salvobioinfo
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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
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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
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Psy-Fer commented Apr 3, 2022

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

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