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ChrisMaherLab / INTEGRATE

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Memory corruption error when supplying dna alignments #3

Open yang-yangfeng opened 6 years ago

yang-yangfeng commented 6 years ago

I am repeatedly getting this error when running Integrate fusion

*** Error in /gscuser/cmiller/usr/src/INTEGRATE_0_2_6/INTEGRATE-build/bin/Integrate': malloc(): memory corruption: 0x00000002d8ce5ff0 ***

Here is my command: ~cmiller/usr/src/INTEGRATE_0_2_6/INTEGRATE-build/bin/Integrate fusion /gscmnt/gc2764/cad/HCC1395/arvados/refseq/GRCh38DH/GRCh38_full_analysis_set_plus_decoy_hla.fa /gscmnt/gc2142/griffithlab/yafeng/cwl_toil_runs/refs/annot.ensembl.GRCh38.txt /gscmnt/gc2142/griffithlab/yafeng/cwl_toil_runs/bwts /gscmnt/gc2142/griffithlab/yafeng/cwl_toil_runs/unstranded/tophat_out/accepted_hits_reordered_fixed.bam /gscmnt/gc2142/griffithlab/yafeng/cwl_toil_runs/unstranded/tophat_out/unmapped.bam /gscmnt/gc2736/griffithlab_gms/yafeng_pvactools/tumor/Final.bam /gscmnt/gc2736/griffithlab_gms/yafeng_pvactools/normal/Final.bam

Any ideas what's going on?

yang-yangfeng commented 6 years ago

I noticed that this error always occurs right as Integrate starts "Processing DNA Tumor..." I tried the test data in order to see if there was something wonky with my inputs. However, I'm not even able to get to that stage because Integrate segfaults on "Getting BWTs for genes in the graph...".

Here is the test command. I ran mkbwt on reference.fasta to make bwts. The supplied test annot.ensembl/ucsc.test.txt do not work as they have 9 columns instead of the required 11. Instead, I downloaded annot.ensembl.txt from the link provided on sourceforge (https://sourceforge.net/projects/integrate-fusion/files/annot.ensembl.txt/download). Everything else directly comes from the provided test inputs.

~cmiller/usr/src/INTEGRATE_0_2_6/INTEGRATE-build/bin/Integrate fusion test-data/reference.fasta annot.ensembl.txt /gscuser/tli/gc3018/genome/bwts/ test-data/accepted_hits.bam test-data/unmapped.bam test-data/dna.tumor.bam test-data/dna.normal.bam