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roblanf / minion_qc

Quality control for MinION sequencing data
MIT License
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Latest Guppy sequencing_summary.txt incompatible with MinIONQC.R #53

Closed stroehleina closed 3 years ago

stroehleina commented 3 years ago

Hi Rob, I re-basecalled a data set with the latest Guppy version (4.0.11+f1071ce) today and when I tried to run MinIONQC.R the script failed with the following error:

INFO [2020-11-27 10:50:21] Loading input file: sequencing_summary.txt
Warning: 1 parsing failure.
     row col   expected    actual                     file
10623384  -- 20 columns 2 columns 'sequencing_summary.txt'

Error in if (max(d$channel) <= 512) { : 
  missing value where TRUE/FALSE needed
Calls: single.flowcell -> load_summary
Execution halted

I compared the old sequencing_summary.txt with the new one and found that the latest version creates a 20-column instead of an 18-column sequencing_summary.txt file. The two additional columns (19 and 20) are:

scaling_median_template scaling_mad_template

When I removed them (cut -f1-18 sequencing_summary.txt) the script worked fine. I am sure this is a very easy fix, just wanted to let you know.

Best wishes, Andreas

stroehleina commented 3 years ago

Closing this as a non-issue, seems like the reason was a corrupt data transfer, not the new file format. Reran with the 20-column file and is working fine. Sorry about that.

Regards, Andreas

roblanf commented 3 years ago

Hi Andreas,

No problem! Much prefer that people raise issues when they find them.

Rob

On Fri, 27 Nov 2020 at 12:04, Andreas Stroehlein notifications@github.com wrote:

Closing this as a non-issue, seems like the reason was a corrupt data transfer, not the new file format. Reran with the 20-column file and is working fine. Sorry about that.

Regards, Andreas

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