Question: Cufflinks segmentation fault
0
gravatar for snp87
2.8 years ago by
snp8740
snp8740 wrote:

Hello! I am trying to run cufflinks on some tophat output files and keep getting a segmentation fault. I intalled cufflinks using homebrew.

Command used: cufflinks -o cufflinks_1 tophat_out1/accepted_hits.bam Error: You are using Cufflinks v2.2.1, which is the most recent release. [14:17:02] Inspecting reads and determining fragment length distribution. Segmentation fault: 11

Can anyone help me rectify this?

Thank you!

rna-seq cufflinks • 1.4k views
ADD COMMENTlink written 2.8 years ago by snp8740

Can you try the binary for OS X downloaded directly from here?

ADD REPLYlink written 2.8 years ago by genomax65k

I tried that but I kept getting the same error. So I converted the BAM files to SAM files and tried the command again (cufflinks -o cufflinks_1 1_accepted_hits.sam). Initially it said: "[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). File 1_accepted_hits.sam doesn't appear to be a valid BAM file, trying SAM..."

But it continued with the processing. Do you think this would cause any problems? Also, do I need to add the mouse genome gtf file to the command? I was seeing different versions of the cufflinks command and wanted to make sure I was doing it properly. Thanks for the help!

ADD REPLYlink written 2.8 years ago by snp8740
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