SOAPsnpZ error : 'std::out_of_range'

ashNZ

Member

Join Date: May 2013

Posts: 11
- Share
- Tweet
#1

SOAPsnpZ error : 'std::out_of_range'

10-09-2013, 06:17 AM

Gday all,

I am attempting to use SOAPsnpZ to call SNPs from SOLiD data that I aligned using SOAP2. After conducting the alignment I 'sorted' the output .txt file and when I try to feed it into the SNP caller I am getting this error message pretty much straight after program execution:

Reading Chromosome and dbSNP information Done.
terminate called after throwing an instance of 'std:ut_of_range'
what(): basic string::substr

Can anyone help me to solve this problem? It would be greatly appreciated! This is my first time using SOAP so I am still very much a beginner.

Cheers
Ash

Last edited by ashNZ; 10-09-2013, 06:21 AM.
Tags: soap, soap assembly sequencing, soap2, soapaligner, soapsnp
IBseq

Member

Join Date: Jul 2012

Posts: 56
- Share
- Tweet
#2

11-30-2017, 10:14 AM

hi
did you get an answer?

ib

Originally posted by ashNZ View Post

Gday all,

I am attempting to use SOAPsnpZ to call SNPs from SOLiD data that I aligned using SOAP2. After conducting the alignment I 'sorted' the output .txt file and when I try to feed it into the SNP caller I am getting this error message pretty much straight after program execution:

Reading Chromosome and dbSNP information Done.
terminate called after throwing an instance of 'std:ut_of_range'
what(): basic string::substr

Can anyone help me to solve this problem? It would be greatly appreciated! This is my first time using SOAP so I am still very much a beginner.

Cheers
Ash
Comment

Previous template Next

Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM
From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data

by SEQadmin2

Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...
- Channel: Articles
06-02-2026, 10:05 AM

Topics	Statistics	Last Post
Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2 Started by SEQadmin2, Yesterday, 11:10 AM	0 responses 7 views 0 reactions	Last Post by SEQadmin2 Yesterday, 11:10 AM
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, 06-17-2026, 06:09 AM	0 responses 42 views 0 reactions	Last Post by SEQadmin2 06-17-2026, 06:09 AM
Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2 Started by SEQadmin2, 06-09-2026, 11:58 AM	0 responses 102 views 0 reactions	Last Post by SEQadmin2 06-09-2026, 11:58 AM
A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2 Started by SEQadmin2, 06-05-2026, 10:09 AM	0 responses 125 views 0 reactions	Last Post by SEQadmin2 06-05-2026, 10:09 AM

Unconfigured Ad

SOAPsnpZ error : 'std::out_of_range'

Comment

Latest Articles

ad_right_rmr

News