whats the solution for this error in Naive Variant Caller (NVC) in usegalaxy?
Traceback (most recent call last):
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__nvc@0.0.4/bin/naive_variant_caller.py”, line 94, in
if name == “main”: main()
File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__nvc@0.
I think this is not the full error message. If you click on that bug icon of the file that gives the error you can see more details.
Traceback (most recent call last):
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__nvc@0.0.4/bin/naive_variant_caller.py”, line 94, in
if name == “main”: main()
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__nvc@0.0.4/bin/naive_variant_caller.py”, line 89, in main
allow_out_of_bounds_positions=options.allow_out_of_bounds_positions, safe=options.safe )
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__nvc@0.0.4/lib/python2.7/site-packages/pyBamTools/genotyping/naive.py”, line 74, in init
self._reference_sequences = IndexedReferenceSequences( reference_sequence_filename, sequence_filter=string.upper )
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__nvc@0.0.4/lib/python2.7/site-packages/pyBamParser/fasta/init.py”, line 23, in init
self._fh = open( filename )
IOError: [Errno 2] No such file or directory: ‘/cvmfs/data.galaxyproject.org/byhand/bosTau7/sam_index/bosTau7.fa,/galaxy/data/bosTau7/sam_index/bosTau7.fa’
Hi @agrieng3
Are you really mapping/calling variants against the cow genome? Or maybe you choose that database by accident? It isn’t supported by many tools anymore, including mapping tools in Galaxy.
That said, there is a technical problem – the path to the genome’s index is wrong. I’ll follow up on that, it may be impacting more than this database.
If using a custom reference genome or calling variants with a BAM dataset that you generated/uploaded, you’ll need to use the tool differently – and that usage (probably) wouldn’t hit the path problem. Let us know and provide a few more details: which reference genome, the source, version, mapped in Galaxy or somewhere else(?), how was the BAM created (which tool)?
Thanks!
Resolution
Please try a rerun now.
Small bit of extra advice unless you were doing this on purpose for some reason (exploratory?): The genome build (database) that you map against shouldn’t have the resulting BAM be modified to be some other build (some tools do interpret the “database” without you choosing). And tool form parameters should not be directly set as being anything other than the exact reference genome the BAM results (content) are actually based on when tools do not automatically interpret the “database” of the input(s).
NVC requires that you set the “database” yourself (and it can be a custom genome build’s “database” specific to your account, if you want to use some genome not natively indexed on the server) or you can just choose the original custom genome fasta dataset instead for that tool (but not all tools, some do require a “database” is assigned).
Coordinates change between genome releases, even if the chromosome names are the same (or mostly the same). Variant analysis would be particularly, and negatively, impacted by that kind of mismatch – meaning, the result would be scientifically invalid, even if the tool did not fail.
Update
We are working to correct this right now. The problem is not just impacting this genome or just this tool. More feedback very soon. Thank you for posting back the full error message! Very helpful 
Yes, cow genome and BosTau7 in locally cached. Bowtie2 use for mapping.
thank you.
Maybe I was looking at some older runs that were mapped against bosTau6 but were assigned to the bosTau7 database. Perhaps a prior mixup
Thank you again for reporting the error! There was definitely a server-side path issue contributing to the error (specifically, paths to certain reference indexes this and other tools use). Those are now corrected.