Segmentation fault while running RNASEQ sample alone
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I'm getting segmentation fault error when i'm trying to run Integrate software on mRNASeq samples (In the past i ran it successfully on other samples)
/data2/labdev/mgf/dev/naresh/MGF/RNASEQ_DELETION/INDEL_SOMATICSNV/Workflow_data/INTEGRATE_0_2_0/Integrate/INTEGRATE-build/bin/Integrate fusion /data2/labdev/mgf/dev/references/hg19/37.1_allchr.fa /data2/labdev/mgf/dev/naresh/MGF/RNASEQ_DELETION/INDEL_SOMATICSNV/Workflow_data/INTEGRATE_0_2_0/Integrate/INTEGRATE-build/bin/annot.ucsc.txt /data2/labdev/mgf/dev/zxs_analysis/lungad/rnaseq_5samp_10_22_2015/output2/ALIGNMENT/STAR1/bwts ../SRR950078.GSNAP.gatkin.bam ../SRR950078.GSNAP.gatkin.bam
INTEGRATE version 0.2.0
Loading reference...
chr1 1 249250621
chr2 249250622 492449994
chr3 492449995 690472424
chr4 690472425 881626700
chr5 881626701 1062541960
chr6 1062541961 1233657027
chr7 1233657028 1392795690
chr8 1392795691 1539159712
chr9 1539159713 1680373143
chr10 1680373144 1815907890
chr11 1815907891 1950914406
chr12 1950914407 2084766301
chr13 2084766302 2199936179
chr14 2199936180 2307285719
chr15 2307285720 2409817111
chr16 2409817112 2500171864
chr17 2500171865 2581367074
chr18 2581367075 2659444322
chr19 2659444323 2718573305
chr20 2718573306 2781598825
chr21 2781598826 2829728720
chr22 2829728721 2881033286
chrX 2881033287 3036303846
chrY 3036303847 3095677412
chrM 3095677413 3095693981
2.75 seconds
Loading genes...
78827 transcripts loaded.
0.56 seconds
Loading BWTs for chromosomes...
51.92 seconds
Handling RNA data...
Insert sizes and stds tested by different RGs:
group1 0 985
Getting graph by encompassing RNA reads...
Segmentation fault
please give me some suggestions.
Regards
Naresh
Are the BAMs for other successful finished samples prepared the same way as the mRNAseq samples?
All mRNAseq samples failed or just one?
Yes they were prepared the same way (aligner GSNAP).
All new samples got failed.