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bioinformatics-centre / bayesembler

A Bayesian method for doing transcriptome assembly from RNA-seq data
MIT License
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core dump when removing duplicates #15

Open sdjebali opened 9 years ago

sdjebali commented 9 years ago

Hi, I am trying to run Bayesembler on a tophat2 (2.0.8) generated file from human K562 whole cell polya+ RNAseq (dUTP protocol): https://www.encodeproject.org/files/ENCFF412EYU/@@download/ENCFF412EYU.bam

Here is the command I ran on a SGE cluster: ~/bin/bayesembler_v1.2.0_linux_x86_64/bayesembler -b $bam -o K562_wcell_polya+_biorep1_cshl_tophat2 -p 4 -s first 2> bayesembler.err where $bam refers to the above bam file

and I get this in the system error file /usr/share/univage/soldierantcluster/spool/node-hp0100rg/job_scripts/1424097: line 3: 39971 Aborted (core dumped) ~/bin/bayesembler_v1 .2.0_linux_x86_64/bayesembler -b /users/rg/jlagarde/projects/encode/scaling/whole_genome/3ncod3_production_files/www.encodeproject.org/files/ENCFF412E YU/@@download/ENCFF412EYU.bam -o K562_wcell_polya+_biorep1_cshl_tophat2 -p 4 -s first 2> bayesembler.err

this in the standard error: bayesembler: /seqdata/krogh/jola/projects/transcriptome_assembly/code/release/bayesembler_1_2_0/src/assembler.cpp:460: std::vector<std::pair<std::list

, std::basic_string > > Assembler::generateSpliceGraphs(double*): Assertion `!current_alignment.IsFailedQC()' failed. and a core file of 80M Please let me know if I did something wrong or if you need more information to solve the problem? thanks sarah
lassemaretty commented 9 years ago

Dear Sarah,

Thank you for posting - and sorry for the late reply. The issue is that your alignment file contains alignments that have the "failed QC-flag" set. We haven't come across this flag actually being set by an aligner before and we thus do not have a mechanism implemented for handling these alignments (but asserts that it is not set which is why the program crashes). What version of Tophat did you run?

We will try to have a minor update out that fixes this within the next week or so. Meanwhile, a quick fix for you would be to simply filter out alignments with this flag set before running the bayesembler. I hope this solves your problem.

Best, Lasse

sdjebali commented 9 years ago

Thank you very much for your answer. I think version 2.0.8 of tophat was run but it was not by me. Anyway I can wait for the fix, this is fine. Thanks, Sarah