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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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"Segmentation fault" error #393

Open sen1019san opened 1 year ago

sen1019san commented 1 year ago

Hi, I am trying to assemble RNA-seq data for gene annotation using StringTie. But the program fails returned the "Segmentation fault" error. The program stop at the Chr1:17731527-19123574 site as followings:

[03/24 01:33:51]>bundle Chr1:17731527-19123574 [18873741 alignments (1578956 distinct), 6571 junctions, 0 guides] begins processing...

The alignment bam file is a merge type with long and short RNA-seq data. The StringTie command is followings:

stringtie {input.merge_rnaseq_bam} --mix -j 3 -c 3 -o {output.merge_rnaseq_gtf}

I have tried to get the stop bundle file using only one thread with -p 1 following the instructions here Extracting bundle data for debugging. This is the bam file I extracted from the stop site:

samtools view -b merge_rnaseq.bam Chr1:17731527-19123574 > bundle_c1.bam

The extracted bundle_c1.bam file is shared in dropbox: https://www.dropbox.com/s/efl4wnpdsokz4uj/bundle_c1.bam?dl=0

I wish the problem to be solved quickly.