virtool/virtool

General user support and discussion

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!

Ian Boyes

@igboyes

@Lafond-LapalmeJ 3.9.8 is available

Joel Lafond-Lapalme

@Lafond-LapalmeJ

Thank you @igboyes !

Ian Boyes

@igboyes

Thank you for reporting the issue @Lafond-LapalmeJ. Please star us on GitHub if you like Virtool.

Abdallah Meknas

@abdallahmeknas_gitlab

Hello,
I was wondering if there was a way to extract the sequences matched by pathoscope into a fasta or txt file for further analysis?

Ian Boyes

@igboyes

Hi. No that is not currently possible as no assembly is performed. Please submit an issue on GitHub if you would like to see this feature added.

Please star Virtool on GitHub if you find it useful.

Abdallah Meknas

@abdallahmeknas_gitlab

ok thank you! @igboyes

Annelies Haegeman

@ahaegeman_gitlab

Hi! Is there a way to make a custom reference database, i.e. upload a fasta with for example 1000 sequences, each one to be treated as a seperate OTU?

Ian Boyes

@igboyes

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.

Annelies Haegeman

@ahaegeman_gitlab

Ok thanks, that's clear! Will raise an issue on GitHub.

abracarambar

@abracarambar

Hi, is there a way of running Virtool remotely from the command line only? And then download results at the end?

Ian Boyes

@igboyes

@abracarambar Please take a look at the API Docs and see if that would meet your needs.

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