fast5_subset on vbz compressed fast5 files

[Ganthark]

Hi,

I was not able to run the fast5_subset on vbz compressed files.
Here is the command I ran (on multiple samples a cluster):
fast5_subset -f "reads" -i $fast5 -s $dir -l "${dir}/ids.txt"
And the output for one of the samples:
Traceback (most recent call last): File "/home/cmatteoli/anaconda3/envs/Nanopore/bin/fast5_subset", line 8, in <module> sys.exit(main()) File "/home/cmatteoli/anaconda3/envs/Nanopore/lib/python3.6/site-packages/ont_fast5_api/conversion_tools/fast5_subset.py", line 313, in main recursive=args.recursive, file_list_file=args.file_list, follow_symlinks=not args.ignore_symlinks) File "/home/cmatteoli/anaconda3/envs/Nanopore/lib/python3.6/site-packages/ont_fast5_api/conversion_tools/fast5_subset.py", line 52, in __init__ "No input fast5 files found in {}. Recursion is set to {}".format(str(input_folder), recursive)) ValueError: No input fast5 files found in ../../../raw/Nanopore/Bd21/191012_Bd21-3/fast5/. Recursion is set to False
A little command to be sure the files are there:
$ ls ../../../raw/Nanopore/Bd21/191012_Bd21-3/fast5/ | head -n 3 FAL51305_884535b6c19bcad13a639b636b466d83fb00966a_0.fast5.vbz FAL51305_884535b6c19bcad13a639b636b466d83fb00966a_100.fast5.vbz FAL51305_884535b6c19bcad13a639b636b466d83fb00966a_101.fast5.vbz

Maybe the extension I used is the problem? I ran other analysis on these files without any issue (mapping, nanopolish...) and I never had issues to subset fast5 before using the vbz compression.

Thank you for this great tool, I hope you can help!

[fbrennen]

Hi @Ganthark -- thanks for letting us know. We'll have a look.

[fbrennen]

Just to confirm, are you sure you're running fast5_subset from the same directory you're running that ls command from? We aren't displaying the absolute path of the input folder in that error message, which isn't very helpful (we'll fix that), so I can't tell just by looking what directory fast5_subset was run from.

[fbrennen]

Ah, sorry, I see the issue -- your files have the wrong extension! They need to end with .fast5, not .vbz.

[Ganthark]

I thought that might be the issue but I wanted to be sure before renaming everything.
Thank you for the quick response!