Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

base calling error #116

Open
oohas2000 opened this issue Sep 8, 2023 · 1 comment
Open

base calling error #116

oohas2000 opened this issue Sep 8, 2023 · 1 comment

Comments

@oohas2000
Copy link

Hi, I have this following error while executing preprocess:
[9c/129f0f] process > baseCalling (guppy-RedOak_WGA-0) [100%] 1 of 1, failed: 1 ✘
[- ] process > concatenateFastQFiles -
[- ] process > QC -
[- ] process > fastQC -
[- ] process > mapping -
[- ] process > counting -
[- ] process > joinCountQCs -
[- ] process > alnQC -
[- ] process > joinAlnQCs -
[- ] process > alnQC2 -
[- ] process > multiQC -
Skipping the email

MultiFast5 files detected!
WARN: The echo directive has been deprecated - use to debug instead
Error executing process > 'baseCalling (guppy-RedOak_WGA-0)'

Caused by:
Process baseCalling (guppy-RedOak_WGA-0) terminated with an error exit status (255)

Command executed:

guppy_basecaller --flowcell FLO-MIN106 --kit SQK-LSK109 --fast5_out -i ./ --save_path ./0_out --cpu_threads_per_caller 1 --gpu_runners_per_device 1 --num_callers 8
cat 0_out/.fastq >> 0.fastq
rm 0_out/
.fastq
gzip 0.fastq

Command exit status:
255

Command output:
(empty)

Command error:
Unexpected token '--fast5_out' on command-line.
Try 'guppy_basecaller --help' for more information.

Work dir:
/nfs/data/projects/Xylella/master_of_pores/NanoPreprocess/work/9c/129f0ff9f8a6d830a50964470517c3

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

@lucacozzuto
Copy link
Member

likely a problem of guppy versions. Please have a look at the new version of MoP

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants