Closed Kamouyiaraki closed 3 years ago
I'll look at it more in depth later, but guppy should be totally fine. I haven't touched albacore since forever :-)
Thanks I appreciate it! For extra info this was a Flongle run (although I don't know why that would matter) and I updated to NanoPlot 1.35.1 just in case it was version issue but I get the same error message,
Do you think it would be possible to share that summary file, or e.g. the first 1000 lines (assuming that subset does replicate the error)?
Annoyingly it did work with the first 1000! But I have to thank you for that, because I then tried to subsample a random 1000 and found that the last 2k lines were all unrecognisable symbols (I'm guessing the file must have been corrupted at some point during the transfer?). Transfered over a new copy from my back up and it's working perfectly. Sorry for the hassle - TIL the usefulness of using tail
Hmmm, good to hear the issue is solved! Annoyingly, corrupted files do happen from time to time...
Hi,
I know this has been asked before, but I can't see to spot where I've gone wrong.
NanoPlot --summary sequencing_summary.txt -o ./Data_pre-processing/Nanoplot_output --readtype 1D --verbose
and I get the error: "ERROR: expected columns in summary file sequencing_summary.txt not found: channel, start_time, duration, sequence_length_template, mean_qscore_template"
Log messages:
My sequencing_summary.txt:
Edit: I have a feeling this has to do with the fact that I have basecalled again using guppy and not Albacore. Not sure what the difference in summary files would be and would rather not have to use Albacore in order to use NanoPlot.
Any insights will be greatly appreciated!