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  • Apr 03 23:04
    igboyes assigned #82
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Joel Lafond-Lapalme
@Lafond-LapalmeJ

Hello,
I have used virtool 3.9.6 for the past 5-6 weeks and it worked well. But since 2 weeks I have an issue when creating a new sample at step Parse FastQC
Here is the error I have:

Traceback (most recent call last):
File "/drone/src/virtool/jobs/job.py", line 166, in run
File "/drone/src/virtool/jobs/create_sample.py", line 104, in parse_fastqc
File "/drone/src/virtool/jobs/fastqc.py", line 127, in parse_fastqc
File "/drone/src/virtool/jobs/fastqc.py", line 182, in handle_base_quality_nan

ValueError: Could not parse base quality values

We installed virtool on a ubuntu 18

Someone ever had a similar issue?
Ian Boyes
@igboyes
Hi @Lafond-LapalmeJ. I will look into this for you.
Ian Boyes
@igboyes
@Lafond-LapalmeJ I will release 3.9.7 tomorrow, which will log the line that is tripping up the FastQC parser.
Joel Lafond-Lapalme
@Lafond-LapalmeJ
Thanks for the quick response.
Ian Boyes
@igboyes
@Lafond-LapalmeJ 3.9.7 should be available for install now. Let me know the quality values that are causing the error. Is there anything unusual about the run/sample?
Joel Lafond-Lapalme
@Lafond-LapalmeJ

I have installed 3.9.7. Here the error I get:

ValueError: Could not parse base quality values '245-249,NaN,NaN,NaN,NaN

what means 245-249 ? line number or sequence number?

Joel Lafond-Lapalme
@Lafond-LapalmeJ
I found the error.
My fastq file has only N in base position over 245. So the fastqc report contains NaN for position 245-249 for the metric Per base sequence content. I can send you the fastqc report or the fastq file if you need it to reproduce the bug.
Thanks for your help.
Ian Boyes
@igboyes
@Lafond-LapalmeJ Thanks. The fastq file would be very helpful to test the changes. How do you want to share it? I can create a file request on Dropbox if that works for you.
Joel Lafond-Lapalme
@Lafond-LapalmeJ
Yess I will put a small sample of the file and make sure the problem is occuring.
Ian Boyes
@igboyes
@Lafond-LapalmeJ Here's the request link: https://www.dropbox.com/request/4wEYyMrd3vinNy64AoH9
Joel Lafond-Lapalme
@Lafond-LapalmeJ
done
Ian Boyes
@igboyes
I will check it out. It may take 1-2 days to release the fix.
Joel Lafond-Lapalme
@Lafond-LapalmeJ
Thanks for your help!