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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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NeoFuse fails because output is not stored in MHC_I and MHC_II folders #26

Closed mantczakaus closed 1 year ago

mantczakaus commented 1 year ago

NeoFuse fails on the step where it's supposed to change the names of the files, i.e. 

mv patient1/NeoFuse/MHC_I/patient1_MHCI_filtered.tsv patient1/NeoFuse/MHC_I/patient1_NeoFuse_MHC_Class_I_filtered.tsv
mv patient1/NeoFuse/MHC_I/patient1_MHCI_unfiltered.tsv patient1/NeoFuse/MHC_I/patient1_NeoFuse_MHC_Class_I_unfiltered.tsv
mv patient1/NeoFuse/MHC_I/patient1_unsupported.txt patient1/NeoFuse/MHC_I/patient1_NeoFuse_MHC_Class_I_unsupported.txt
mv patient1/NeoFuse/MHC_II/patient1_MHCII_filtered.tsv patient1/NeoFuse/MHC_II/patient1_NeoFuse_MHC_Class_II_filtered.tsv
mv patient1/NeoFuse/MHC_II/patient1_MHCII_unfiltered.tsv patient1/NeoFuse/MHC_II/patient1_NeoFuse_MHC_Class_II_unfiltered.tsv
mv patient1/NeoFuse/MHC_II/patient1_unsupported.txt patient1/NeoFuse/MHC_II/patient1_NeoFuse_MHC_Class_II_unsupported.txt
mv patient1/NeoFuse/MHC_II/patient1_mixMHC2pred_conf.txt patient1/NeoFuse/MHC_II/patient1_NeoFuse_MHC_Class_II_mixMHC2pred_conf.txt

These files are not created. The NeoFuse folder contains two files only and no folders (which is consistent with what described in the current NeoFuse manual https://github.com/icbi-lab/NeoFuse#325-neofuse):

patient1_filtered.tsv
patient1_unfiltered.tsv

So the error I'm getting is: mv: cannot stat 'patient1/NeoFuse/MHC_I/patient1_MHCI_filtered.tsv': No such file or directory

mantczakaus commented 1 year ago

I realised I might be using a wrong container! Let me recheck that. If that's the case, I'll close the issue.