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bioinformatics-centre / bayesembler

A Bayesian method for doing transcriptome assembly from RNA-seq data
MIT License
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Error in Bayesembler v1.2.0 #12

Open jpkoskin opened 9 years ago

jpkoskin commented 9 years ago

Hi,

I'm trying to test Bayesembler, but so far with no successful results. My data is paired-end and I did run Tophat2 with default parameters. Still I'm getting error messages like following:

$ bayesembler -b tophat_out/accepted_hits.bam -o Bayes_test

You are using the Bayesembler v1.2.0. For more information go to bayesembler.binf.ku.dk

bam_nd_pe_plus_file_nameBayes_testaccepted_hits_nd_plus.bam [12/06/2015 11:23:05] Removing duplicate reads bayesembler: /seqdata/krogh/jola/projects/transcriptome_assembly/code/release/bayesembler_1_2_0/src/assembler.cpp:336: std::vectorstd::pair<std::list<GraphInfo, std::basic_string > > Assembler::generateSpliceGraphs(double*): Assertion `current_alignment.IsPaired()' failed. Aborted

What is wrong and how do I fix this?

best, Patrik

jpkoskin commented 9 years ago

Is there a hard coded path that should be changed?

lassemaretty commented 9 years ago

Hi Patrik,

Sorry about your issue with the Bayesembler - and thank you for letting us know!

Im not exactly sure what is causing your problem. First, maybe try rerunning TopHat with --no-mixed and see if it that fixes your problem. If that is not the case, I will need to know the exact TopHat2 version and command-line - and, if by any means possible, access to your data or maybe just a sample of it that can reproduce the error.

Thanks again for posting,

Lasse