There were problems in parsing your input file with the following rows

[thecorz]

Hi Rob,

I have joined multiple sequencing_summary.txt files via cat and pipe >. But the script is throwing an error, don't really know what it is about, but my guess is related to the formating of the summary files that might have been changed.

This is the error message

There were problems in parsing your input file with the following rows: 

WARN [2022-12-08 12:11:39] 3773657
.
.
.

These rows will be ignored for further analysis, please check your input file
Error in if (max(d$channel) <= 512) { : 
  missing value where TRUE/FALSE needed
Calls: single.flowcell -> load_summary
Execution halted

Any ideas of what has caused it?

Thanks

[roblanf]

If you're using cat you might be adding in multiple header rows? If not, then yes it could be that the format has changed. Unfortunately the format changes a lot, and the latest is that the summary file might be scrapped all together, so tools like MinIONQC won't be useful any more.

…

On Thu, 8 Dec 2022 at 23:16, Javier Cuadrado Corz ***@***.***> wrote: Hi Rob, I have joined multiple sequencing_summary.txt files via cat and pipe >. But the script is throwing an error, don't really know what it is about, but my guess is related to the formating of the summary files that might have been changed. This is the error message `There were problems in parsing your input file with the following rows: WARN [2022-12-08 12:11:39] 3773657 . . . These rows will be ignored for further analysis, please check your input file Error in if (max(d$channel) <= 512) { : missing value where TRUE/FALSE needed Calls: single.flowcell -> load_summary Execution halted` Any ideas of what has caused it? Thanks — Reply to this email directly, view it on GitHub <#60>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG2SE7USWAC6VD2CV3OVOLWMHGTJANCNFSM6AAAAAASYCDYBA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra www.robertlanfear.com

[KylonisThanos]

Hello guyz ! i just intalled the minionqc through conda and i got the same error message . i had 5 files and i used cat command . but when i deleted the 4 header rows it did run without error messages . could we possibly to something so we can overcome this problem with cat? use another command or predict tis throught the script itself?

[roblanf]

Hi @KylonisThanos - unfortunately I don't have capacity at the moment to build this in. But if you'd like to submit a pull request for this I'll happily take a look.

I'll leave this issue open because its' been on my mind that the whole thing could use a rebuild and a speed up, and this is certainly something that could be fixed as part of that.