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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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Segmentation fault (core dumped) #26

Open fzhang005 opened 7 years ago

fzhang005 commented 7 years ago

Hi Qing，

When I run giremi, I got the following error: Segmentation fault (core dumped). I don't know if it's the problem of the SNV list, please see the attached file. Thanks.

Best, Fan

SRR307897.txt

zhqingit commented 7 years ago

Hi Fan,

It looks your SNV list is ok. How much memory do you use?

Best, Qing

2016-10-17 21:36 GMT-07:00 fzhang005 notifications@github.com:

Hi Qing，

When I run giremi, I got the following error: Segmentation fault (core dumped). I don't know if it's the problem of the SNV list, please see the attached file. Thanks.

Best, Fan

SRR307897.txt https://github.com/zhqingit/giremi/files/535267/SRR307897.txt

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fzhang005 commented 7 years ago

Hi Qing,

Thanks for reply. I used a cluster and applied for 60G memory to run GIREMI.

Best, Fan

zhqingit commented 7 years ago

Hi Fan,

Are you using linux 64? Can you send me a piece of bam file and your command?

Best, Qing

2016-10-17 23:52 GMT-07:00 fzhang005 notifications@github.com:

Hi Qing,

Thanks for reply. I used a cluster and applied for 60G memory to run GIREMI.

Best, Fan

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fzhang005 commented 7 years ago

Hi Qing,

Yes, it's a 64bit linux. Please find the first 1k lines in the bam file. My command is: giremi -f ${fastaPath}/hg19.fa -l SRR307897.txt -o ${outPathGiremi}.res -p 1 -m 5 -s 0 SRR307897_callOut.bam

SRR307897_callOut_1k.bam.txt

fzhang005 commented 7 years ago

Hi Qing,

Now the problem is still there. Could you give me some suggestions on it? BTW, could you share your complete scripts for running GIREMI to us? Thanks a lot.

Best, Zhang Fan

zhqingit commented 7 years ago

Hi Fan,

I think it's related to your system. I have tried the sample and the command you send to me, there is no any issue. I wonder if you can try giremi in other computers?

Best, Qing

2016-10-30 20:01 GMT-07:00 fzhang005 notifications@github.com:

Hi Qing,

Now the problem is still there. Could you give me some suggestions on it? BTW, could you share your complete scripts for running GIREMI to us? Thanks a lot.

Best, Zhang Fan

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fzhang005 commented 7 years ago

Hi Qing,

Thanks for your suggestion. I will try on other platform.

Best, Zhang Fan

JohnMCMa commented 7 years ago

Hi @fzhang005 , I wonder what is the output if you run picard ValidateSam on your bam file? At one point I have the same problem, but I have been able to isolate it to an BAM file issue.

fzhang005 commented 7 years ago

Hi @JohnMCMa, thanks for your suggestion, but my problem should be caused by the server, although I couldn't find out the exact reason, I have managed to run after changed to another server.

Best, Zhang Fan

fzhang005 commented 7 years ago

Hi @zhqingit ,

May I ask another question, is there any other filter in the GIREMI besides SNP? Such as separating Alu and nonAlu, removal of the sites near to splicing junctions?

Best. Zhang Fan

zhqingit commented 7 years ago

Hi Fan,

We don't have other filters. Thanks.

Best, Qing

2016-11-22 22:47 GMT-07:00 fzhang005 notifications@github.com:

Hi @zhqingit https://github.com/zhqingit ,

May I ask another question, is there any other filter in the GIREMI besides SNP? Such as separating Alu and nonAlu, removal of the sites near to splicing junctions?

Best. Zhang Fan

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fzhang005 commented 7 years ago

Hi @zhqingit,

Noted with thanks.

Best, Zhang Fan

AMChalkie commented 6 years ago

I also get a core dump, and without knowing what the code is doing it is hard to resolve (tried multiple bam files). Would be useful beyond a core dump to know what step the program is in (allocating memory - how much for example). +1 for helpful error messages.

Comy97 commented 4 years ago

Hi @zhqingit , I also get a segementation fault (core dump) and I have struggled for over one months. I have read several papers your team written but still cannot found the solution. My tutor was mad at me. I am eager to solve the problem. Hope you could help me. Thanks.

Best, Comy Kong

test.txt

test_test_dup2.sam.txt

Comy97 commented 4 years ago

For convenience, I convert the bam file to sam file using samtools. My command is : giremi -p 0 -s 1 -f hg.fa -l test.txt -o RNAE.lst test_test_dup2.bam

jiabowang commented 4 years ago

Hi @zhqingit, I also have this error. Please help us. I can not change to another computer. Hope you can help me.