search

polio-nanopore / piranha

GNU General Public License v3.0
17 stars 4 forks source link

Not urgent - error running wg pipeline #238

Closed CatherineTroman closed 1 month ago

CatherineTroman commented 3 months ago

I was having a go at analysing some single amplicon (~7.3kb) whole genome data from our workshop.

Input the following command: piranha -i ./fastq_pass/ -b ./barcodes-2.csv -m wg -n 7000 -x 7500

It looked like it was running fine then gave the error in the attached text file. It looks like it filtered and mapped the reads fine but stopped before starting consensus building. wg-error-piranha.txt

Many thanks, Catherine

rmcolq commented 3 months ago

Is this in the GUI or on the command line? And is it running in the docker container (assume yes if in GUI)? I believe I have just created a working updated docker container, but I was holding off on merging it while the workshop was ongoing as didn't want to accidentally introduce new bugs.

Can you tell me what is in .snakemake/log/2024-06-21T104211.970855.snakemake.log?

CatherineTroman commented 3 months ago

This is on the command line on ubuntu, I didn't think we could do whole genome as an option on the GUI yet.

I can't seem to find the snakemake log at the moment but will keep looking and add it in when I've found it. Can only see logs from years ago!

rmcolq commented 3 months ago

Ah ok! It probably isn't in the GUI. If you are on the command-line, you will need to run with --no-temp to keep all the logs and intermediate files to debug this (GUI runs in no-temp mode by default) and find the source of the error

CatherineTroman commented 3 months ago

Sorry for the delay. I ran again on the same data using --no-temp

There were two snakemake log files which I have attached. Not sure how useful they are as I had a look and neither seems to say much - unless not having a lot in it means something more.

2024-06-24T165644.936478.snakemake.log 2024-06-24T164625.876267.snakemake.log

aineniamh commented 1 month ago

This should now be resolved on main, wg pipeline is now the same as vp1 pipeline (file piranha_main.smk), and both now include depth masking options. the wg setting finds the relevant reference file and changes configuration slightly (may need to be revised depending on which wg protocols are being run).