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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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double free or corruption (!prev): 0x000000000dd4aaa0 *** #40

Open yang91 opened 6 years ago

yang91 commented 6 years ago

Hi,

I've tried GIREMI on my SNV datasets generated by tophat2+picard+GATK+annovar pipline, while it reported

/home/yangxx/software/giremi-master/giremi': double free or corruption (!prev): 0x000000000d97faa0 *** Segmentation fault (core dumped)

my command is /home/yangxx/software/giremi-master/giremi -f $ref/Homo_sapiens_assembly38.fa -l $path/script/GIREMI/Severe_Early-New.GIREMI.input.txt -p 1 -o /$path/Result/GIREMI/ $path/Result/picard/PHPR0008_L8_I349-NewBatch2/Mark_duplicates.bam.

my SNV inputs are like below:

chr1 16494 16495 WASH7P 1 - chr1 16736 16737 WASH7P 0 - chr1 16741 16742 WASH7P 0 - chr1 16948 16949 WASH7P 1 - chr1 17019 17020 WASH7P 1 - chr1 17279 17280 WASH7P 0 - chr1 17311 17312 WASH7P 0 - chr1 17378 17379 MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4 1 - chr1 17384 17385 MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4 1 - chr1 17397 17398 MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4 1 -

and top command displays of my server like below:

KiB Mem : 13191555+total, 42587552 free, 797532 used, 88530472 buff/cache KiB Swap: 19531212+total, 19436460+free, 947508 used. 13036427+avail Mem

Since JohnMCMa had mentioned in #25 that GATK would achieve local realignment around indels before using HaplotypeCaller to call variants, I've tried to use bam files produced by GATK as bam inputs in GIREMI, while the error remained.

Could anyone give some solutions about it? Thanks very much!