BioPerl error from setup.sh #468

Closed
cmdcolin opened this Issue Apr 23, 2014 · 2 comments

Comments

Projects
None yet
1 participant
@cmdcolin
Contributor

cmdcolin commented Apr 23, 2014

I am getting an error when running setup.sh that says

+ bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: No suitable files found in sample_data/raw/yeast_chr1+2
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/Root/Root.pm:486
STACK: Bio::DB::IndexedBase::index_dir /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/IndexedBase.pm:444
STACK: Bio::DB::IndexedBase::new /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/IndexedBase.pm:361
STACK: Bio::DB::SeqFeature::Store::memory::commit /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/SeqFeature/Store/memory.pm:172
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352
STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK: Bio::DB::SeqFeature::Store::Loader::load /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK: Bio::DB::SeqFeature::Store::memory::post_init /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/SeqFeature/Store/memory.pm:164
STACK: Bio::DB::SeqFeature::Store::new /home/name/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/SeqFeature/Store.pm:395
STACK: Bio::JBrowse::Cmd::BioDBToJson::run /home/name/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm:70
STACK: bin/biodb-to-json.pl:9
-----------------------------------------------------------

We communicated with #bioperl on irc and they confirmed a behavior change that requires us to update jbrowse (thanks trs)

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Apr 23, 2014

Contributor

Chatlog april23rd 2014 confirming a BioPerl behavior change which requires us to have sequence files in the BioDB folder

21:42 < trs> cdiesh: so the issue appears to be that there's no associated fasta file containing the sequence data for the gff file
21:42 < trs> which is required if the sequence data isn't embedded in the gff
21:44 < cdiesh> trs: oo. ok let me see if thats the case here
21:44 < trs> I guess it's a behaviour change
21:45 < cdiesh> trs: ya we don't have the sequence on our gff.
21:45 < cdiesh> is there any workaround, such as having a sequence file in the same folder, or does it need to be in the gff?
21:47 < cdiesh> if i read what you said correctly, then I think that a fasta file could simply be in the folder :)? i will test it out
21:47 < trs> yes
21:55 < cdiesh> trs: looks like that fixes it!
21:56 < cdiesh> for real this time. thank you!
22:00 < trs> cdiesh: the behaviour change happened first in 1.6.910
22:00 < trs> with this bioperl commit 216622f
22:00 < trs> which changed the indexer's behaviour from "return unless @files" to "$self->throw(...) unless @files"
22:01 < trs> "silently don't index anything" to "complain about nothing to index"
Contributor

cmdcolin commented Apr 23, 2014

Chatlog april23rd 2014 confirming a BioPerl behavior change which requires us to have sequence files in the BioDB folder

21:42 < trs> cdiesh: so the issue appears to be that there's no associated fasta file containing the sequence data for the gff file
21:42 < trs> which is required if the sequence data isn't embedded in the gff
21:44 < cdiesh> trs: oo. ok let me see if thats the case here
21:44 < trs> I guess it's a behaviour change
21:45 < cdiesh> trs: ya we don't have the sequence on our gff.
21:45 < cdiesh> is there any workaround, such as having a sequence file in the same folder, or does it need to be in the gff?
21:47 < cdiesh> if i read what you said correctly, then I think that a fasta file could simply be in the folder :)? i will test it out
21:47 < trs> yes
21:55 < cdiesh> trs: looks like that fixes it!
21:56 < cdiesh> for real this time. thank you!
22:00 < trs> cdiesh: the behaviour change happened first in 1.6.910
22:00 < trs> with this bioperl commit 216622f
22:00 < trs> which changed the indexer's behaviour from "return unless @files" to "$self->throw(...) unless @files"
22:01 < trs> "silently don't index anything" to "complain about nothing to index"

@cmdcolin cmdcolin closed this in b735b88 Apr 23, 2014

@cmdcolin cmdcolin added this to the Release 1.11.4 milestone Apr 24, 2014

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin May 2, 2014

Contributor

This commit is also relevant d5b1df2

Contributor

cmdcolin commented May 2, 2014

This commit is also relevant d5b1df2

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment