Segmentation fault (core dumped)

[fzhang005]

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]

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]

Hi Qing,

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

Best,
Fan

[zhqingit]

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]

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]

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]

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]

Hi Qing,

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

Best,
Zhang Fan

[JohnMCMa]

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]

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]

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]

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]

Hi @zhqingit,

Noted with thanks.

Best,
Zhang Fan

[AMChalkie]

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]

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]

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]

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