igboyes on 5.0.0
Setup Sentry performance monito… (compare)
igboyes on 5.0.0
Improve all typing (#2257) (compare)
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
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.Hi @ahaegeman_gitlab . No there isn't. Please raise an issue on GitHub if you would like to see this feature.
In the meantime, it would be quite simple to write a script to parse your FASTA file and create the reference via Virtool's HTTP API. The flow for each OTU would be: create_otu, create_isolate, create_sequence.