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[Bug]: QUAST for phased diploid assembly doesn't work #805
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It would help if you could tell us exactly which quast docker image was used as well as the command used to execute quast. Additionally please share an error message (if it exists?). The log file you shared looks like there were only warnings, but no errors? |
Thank you for your fast reply.
This is the command that I have used to run quast, but at the beginning of the log file you can see the exact files and their corresponding formats. The docker version is the latest one, for the 5.2.0 version. Unfortunately no error message has been shown, from the log the process seems to have finished without problems. |
Hi @ChiaraCampanelli,
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This is the log file you asked.
Let me know if you want me to attach the files quast is using. |
I think I spotted the non-zero exit code/error:
I think you'll need to look at this file to see the |
It seems ok? |
It looks like the quast stopped abruptly. "Analysis is finished." prompt is for an individual step. Your working directory is /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/ |
Hmm I wonder if maybe the mapping process didn't finish or ran out of memory or something. Usually you will see some kind of confirmation message that the mapping has finished. Have you re-ran with less CPUs? or request more RAM on the SLURM runner? |
Thank you for your help. |
Unfortunately there are no progresses, despite I have changed the resources as you suggested.
As often happens, the analysis got stuck in the BWA run phase. It's been almost 20 hours that is working without updates. |
I'm not sure what else to suggest here, as I don't typically run quast this way. You could try using a biocontainer docker image for quast, and that would help determine if the issue is caused by the staphb docker image or not. Try the most recent v5.2.0 image from here? https://quay.io/repository/biocontainers/quast?tab=tags If you get the same behavior with the biocontainer docker image, that might mean there's something wrong with your input files or some other cause |
What container were you trying to use, and how were you attempting to use it?
Is anybody know why the tool doesn't work when I give in input the diploid genome?
The diploid genome is generated by using HapDup starting from an assembly done by using long read sequencing data.
From the log file it seems that the analysis is completed but no file has been generated and the process keeps working forever.
Relevant log output
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