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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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Using nanopolish index on a fast5 directory ending with a backslash produces paths that don't exist #1056

Open zigavicic opened 1 year ago

zigavicic commented 1 year ago

So I had problems running nanopolish and decided to build it from the docker image provided at https://quay.io/repository/biocontainers/nanopolish?tab=tags&tag= just to finnaly get it to work. Running nanopolish polya still resulted in an error. So I figured it must be something to do with the nanopolish index and found these errors to confirm it:

#006: H5FDsec2.c line 352 in H5FD__sec2_open(): unable to open file: name = 'results/workspace//FAV19784_a1ccb5ce_052bbeb2_97.fast5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0 major: File accessibility minor: Unable to open file

It turns out running nanopolish index -d path/to/fast5/ -s path/to/sequencing_summary.txt smthn.fastq Produces this path with double forward slashes that then breaks nanopolish polya even though nanopolish index finishes successfully. Maybe you could somehow check for this in nanopolish index function.

jts commented 1 year ago

That's odd, double backslashes shouldn't have any effect in most filesystems. What operating system are you on?