Segmentation fault

[purplerainf]

Hi,

I ran the giremi with the following command, and got an error.

$ ./giremi -f ../reference_seq/chr22.fa -l snp_chr22.txt -o test 400.chr22.bam
[mpileup] 1 samples in 1 input files
error : Can't find the snv!
Segmentation fault (core dumped)

I downloaded the giremi execution through git clone command,
and the bam file includes alignments on Chr 22 only.

I know all issues in here about the Seg fault are due to some errors in SNV list.
But I can't find any problem in my SNV list (it is attached).

Could anyone help me?
If i can get a toy example, it will be very helpful.

Thanks.
YY.

snp_chr22.txt

[zhqingit]

Hi YY,

Could you check if the chromosome name in your SNV list match the name in
the fasta file?

Best,
Qing

2016-05-11 9:51 GMT-07:00 YY notifications@github.com:

Hi,

I ran the giremi with the following command, and got an error.

$ ./giremi -f ../reference_seq/chr22.fa -l snp_chr22.txt -o test
400.chr22.bam
[mpileup] 1 samples in 1 input files
error : Can't find the snv!
Segmentation fault (core dumped)

I downloaded the giremi execution through git clone command,
and the bam file includes alignments on Chr 22 only.

I know all issues in here about the Seg fault are due to some errors in
SNV list.
But I can't find any problem in my SNV list (it is attached).

Could anyone help me?
If i can get a toy example, it will be very helpful.

Thanks.
YY.

snp_chr22.txt
https://github.com/zhqingit/giremi/files/259752/snp_chr22.txt

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#16

[purplerainf]

Contents of the fasta file is as follow.
[ giremi ]$ head chr22.fa

chr22
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...

BTW, I changed all chromosome names in my SNV file from 'chr22' to '>chr22' then
giremi showed a different result. (attached log.txt)
It seems to recognize the SNVs, but segmentation fault again.
log.txt

Thanks,
YY.

[zhqingit]

Hi YY,

Firstly, I think the format of fasta file should be >chr22. And in the SNV
list, the chromosome name should be chr22. Because you only use chr22,
which only generates very few SNV-SNV paris and can't infer a MI
distribution. I suggest you use all the chromosome.

Best,
Qing

2016-05-13 12:08 GMT-07:00 YY notifications@github.com:

Contents of the fasta file is as follow.
[ giremi ]$ head chr22.fa

chr22
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...

BTW, I changed all chromosome names in my SNV file from 'chr22' to
'>chr22' then
giremi showed a different result. (attached log.txt)
It seems to recognize the SNVs, but segmentation fault again.
log.txt https://github.com/zhqingit/giremi/files/263917/log.txt

Thanks,
YY.

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#16 (comment)

[purplerainf]

Sorry Qing.
It must be a mistake when I copied the result to this board.
The name of chromosome is ">chr22", not "chr22"
Sorry for the mistake.

By the way, I have another question.
I used a sorted bam file, which means paired-end reads are far away each other.
Can it cause a problem?

Thanks,
YY.

[zhqingit]

Hi YY,

The sorted bam doesn't cause any problem.

Best,
Qing

2016-05-16 7:47 GMT-07:00 YY notifications@github.com:

Sorry Qing.
It must be a mistake when I copied the result to this board.
The name of chromosome is ">chr22", not "chr22"
Sorry for the mistake.

By the way, I have another question.
I used a sorted bam file, which means paired-end reads are far away each
other.
Can it cause a problem?

Thanks,
YY.

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#16 (comment)

[purplerainf]

Qing,

From the issue #4, I realize that my SNV list contains indels... (which relates with multiple nt.)
After removing the indels, it seems to work well except two strange behaviors.
(please see attached log)

1. it prints out a list of coordinates of SNVs. (in the 3rd and 6th lines in the log file)
2. at the final moment, seg fault occurs again even it seems to be completed well.

Except above two abnormal outputs, it works well and I can get ifRNAE values. (with whole chromosome dataset)
Do you think it works well or still has some problem?

Thanks for your all help.
YY.

log2.txt

[zhqingit]

Hi YY,

I noticed that the output includes many homogeneous SNPs whose allelic
ratio are 1. These sites will cause problem in the prediction. So please
remove them and run giremi again.

Best,
Qing

2016-05-16 12:38 GMT-07:00 YY notifications@github.com:

Qing,

From the issue #4 #4, I
realize that my SNV list contains indels... (which relates with multiple
nt.)
After removing the indels, it seems to work well except two strange
behaviors.
(please see attached log)

1. it prints out a list of coordinates of SNVs. (in the 3rd and 6th lines
   in the log file)
2. at the final moment, seg fault occurs again even it seems to be
   completed well.

Do you think it works well or still has some problem?

Thanks for your all help.
YY.

log2.txt https://github.com/zhqingit/giremi/files/266784/log2.txt

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#16 (comment)

[purplerainf]

Thank you Qing,

When I executed whole chromosome data, I excluded SNVs with extreme allele ratio (>0.9 or <0.1)

I really appreciate your help.
Best regards,
YY.