Question: Problem for pindel2vcf to create VCF file from pindel created _D files
0
gravatar for hongbing.li
3.0 years ago by
Canada
hongbing.li0 wrote:

Hi

I am new pindel user, and use ../pindel -f hg19.fasta -i p1_config.txt -c ALL -o P2_Index_95_P319 to create P2_Index_95_P319 with _SI, _D, and so on. When I use pindel2vcf to create vcf file with _SI. I got it. and also found some interesting insertion. But when I create vcf filw with_D, using "../pindel2vcf -p P2_Index_95_P319_D -r hg19.fasta -R hg19-GRCh37 -d 200902 -v P2_Index_95_P319_D.vcf" , some error is as following:

Exiting reference scanning.

Processing chromosome chr1

Reading region 0-300000000

Reading chromosome chr1 into memory.

terminate called after throwing an instance of 'std::out_of_range'

what(): basic_string::erase

Aborted (core dumped)

It will be appreciated to give suggestion from anybody.  I try other samples, All _SI get its vcf, but _D gives same errors.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by hongbing.li0

chr1 is ~250E6 bp but your tool is trying to read 300E6 bp ? did you write a config file with this '300000000' ?

ADD REPLYlink written 3.0 years ago by Pierre Lindenbaum101k

This was cross-posted on SEQanswers.

ADD REPLYlink written 3.0 years ago by nnutter200

can you communicate with me by email on this? kye@genome.wustl.edu

I need the pindel output lines causing the error. 

ADD REPLYlink written 3.0 years ago by liangkaiye250

Thanks for your remind .

ADD REPLYlink written 3.0 years ago by hongbing.li0

Hi there, I am having a similar problem with pindel2vcf. Here is my command:

/path/to/pindel2vcf -p /path/to/pindel_chrXsubset_D -r /path/to/canFam3.fa -R canFam31 -d 20141204 -v /path/to/pindel_chrXsubset_D.vcf -G

And the output I'm getting is:

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::erase

Thanks for any thoughts you might have.

Steve

ADD REPLYlink written 3.0 years ago by steven_friedenberg10

Problem has been resolved by Lingkaiye.

Thanks for all of you!

ADD REPLYlink written 3.0 years ago by hongbing.li0

Hi.

I experience the same sort of problem. Could you post about how to fix it please?

/winnie

 

My Error message:

Exiting reference scanning.

Processing chromosome P0116_N055-10_trimmed_(paired)_contig_1_consensus

Reading region 0-300000000

Reading chromosome P0116_N055-10_trimmed_(paired)_contig_1_consensus into memory.

terminate called after throwing an instance of 'std::out_of_range'

  what():  basic_string::erase: __pos (which is 60) > this->size() (which is 3)

Abort trap: 6

 

ADD REPLYlink written 3.0 years ago by winnie0

Hi winnie,

Following is resolved by Liangkeye for me

  1. grep ChrID P2_Index_13_P375_D > P2_Index_13_P375_D.head.txt

  2. ../pindel2vcf -p P2_Index_13_P375_D.head.txt -r hg19.fasta -R hg19-GRCh37 -d 200902 -v P2_Index_13_P375_D.head.txt.vcf

I hope this will help you!

Best reagrds,

Hongbing Li

From: winnie on Biostar [mailto:notifications@biostars.org] Sent: December-10-14 8:39 AM To: hongbing.li2011@gmail.com Subject: [biostar] C: Problem for pindel2vcf to create VCF file from pindel created _D files

Activity on a post you are following on Biostar <http: www.biostars.org="">

User winnie <http: www.biostars.org="" u="" 15177=""/> wrote Comment: Problem for pindel2vcf to create VCF file from pindel created _D files <http: www.biostars.org="" p="" 121670="" #123222=""> :

Hi.

I experience the same sort of problem. Could you post about how to fix it please?

/winnie

My Error message:

Exiting reference scanning.

Processing chromosome P0116_N055-10_trimmed_(paired)_contig_1_consensus

Reading region 0-300000000

Reading chromosome P0116_N055-10_trimmed_(paired)_contig_1_consensus into memory.

terminate called after throwing an instance of 'std::out_of_range'

what(): basic_string::erase: __pos (which is 60) > this->size() (which is 3)

Abort trap: 6


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ADD REPLYlink written 3.0 years ago by hongbing.li0

I will give a go. Thank you.

best regards,

Winnie

ADD REPLYlink written 3.0 years ago by winnie0
0
gravatar for hongbing.li
3.0 years ago by
Canada
hongbing.li0 wrote:

Thanks for all your response, and I have sent files to kye@genome.wustl.edu

ADD COMMENTlink written 3.0 years ago by hongbing.li0
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