Issue with .fast5 files from nonopore sequencing

1

Hi,
I am trying to polish my consensus sequences from “Nanopolish variants (Galaxy Version 0.14.0+galaxy0)” tool.

However, I am encountering issues with the .fast5 files.

  1. The .fast5 files are being autodetected as H5 format, which is not accepted by the “Nanopolish variants” tool.
  2. Despite attempting to uncompress or convert the file format to fast5.tar, fast5, or fast5.tar.gz, the files appear as 0 sequences, leading to an error.

“gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now”

Could you please advise on how to resolve this issue?

Thank you
Best regards
Saumya.

2

Hi @l.r.l.s.k

It sounds like the Upload tool is guessing the wrong datatype.

Try Uploading again, and this time select the correct type.

Changing the datatype after Upload can also work but if you have any trouble at all: start over with Upload. Why? compressed data can get into an odd state, and loading again refreshes that.

Hope this helps! :slight_smile: