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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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segmentation fault #54

Open abayega opened 5 years ago

abayega commented 5 years ago

Hi Dadi,

thank u for this tool. I am running into this similar error and I realise that it was not resolved here. I have attached my out put. My versions are gcc (GCC) 5.4.0 STAR-2.6.0c bedtools v2.27.1

I already checked that although my gtf is not Ensemble, each gene has 'gene_type' attribute and each transcript and exon has both 'gene_type' and 'transcript_type' tags

I already checked that although my gtf is not Ensemble, each gene has 'gene_type' attribute and each transcript and exon has both 'gene_type' and 'transcript_type' tags

abayega commented 5 years ago

Kindly assist me to determine where this error is coming from. I am working on a cluster slurm-823887.txt

dg520 commented 5 years ago

Hi @abayega ,

I'm just back from oversea and was blocked to visit GitHub when I was away. I saw you help the other user to solve this problem. Let me know if you have further questions. And thanks a lot for your help.

Best, Dadi

abayega commented 5 years ago

Hi,

welcome back. I still have segmentation faults. I have attached the output files I get. It seems to me that the problem comes from the use of IRFinder to perform the mapping which fails. Genome build is okay but still the mappability seems to fail. Kindly assist me

slurm-910128.out.txt slurm-929828.out.txt

abayega commented 5 years ago

Hi,

could you help me with the pre-compiled IRFinder files? I think I might just need to recompile those file to be able to run on our cluster.