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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Error executing process with NeoFuse #5

Closed antaralabiba97 closed 2 years ago

antaralabiba97 commented 2 years ago

Hi,

I came across your pipeline not long ago and found it would be great for my research so I am really keen to make sure I can get it running.

I set the pipeline up and did not input the HLA-HD file as I wanted to first make sure I could get the pipeline running to predict MHCI neoepitopes first. The only thing I did change was in the process.conf file where I changed the CPU usage for all processes to 40.

I have attached the HTML file detailing the error which stopped the pipeline running at the NeoFuse stage. I went and had a look at the "sample1_MHCI_final.log" file as detailed in the error and the ".command.sh" script file in the working directory stated in the pdf file of the error which I have attached. In the pdf file the first line of the error has been omitted when I converted from HTML to pdf but it stated "Error executing process > 'Neofuse (sample1)".

I was happy that it was running smoothly and the prepoccessing steps had been completed successfully however, unfortunaley an error arised. I am actually not sure how to resolve the error stated and would really appreciate any help.

Thank you in advance!

Nextflow Workflow Report.pdf sample1_MHCI_final.log

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antaralabiba97 commented 2 years ago

After doing what you suggested above, the pVACseq process did start more than 48 hours ago 😅 but many processes have gone defunct straight after starting and the processes which are running have been running for a very long time. Think the best thing to do is to run it on my PC when it arrives as not sure how to overcome the issues with the cluster.

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