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

[michaeldonaldson]

Hi,

I did perform a test using the hg19_v3.0.2/tmp_1.fq/tmp_2.fq files provided in lobstr-code and it did generate test.aligned.bam, test.aligned.stats, test.vcf, and test.allelotype.stats.

I have sequence-capture illumina data and I'm trying to genotype 30 microsatellite loci in a bat species using lobstr. I generated a .bed file using TRF for 30 ~1000 bp regions of that bat genome.

Here's how I created my reference:
python2 lobstr_index.py --str ./lobSTR/bat_lobstr.bed \ --ref ./lobSTR/bat_str.fasta --out ./lobSTR/lobref/ --extend 500 python2 GetSTRInfo.py ./lobSTR/bat_lobstr.bed \ /home/user/workspace/lobSTR/bat_str.fasta > ./lobref/strinfo.tab

Here are my commands for the alignment:
lobSTR --extend 500 \ --p1 2004-AR-40_R1.fastq \ --p2 2004-AR-40_R2.fastq \ --fastq --index-prefix ./lobref/lobSTR_ --out 2004-AR-40 \ --rg-sample 2004-AR-40 --rg-lib 2004-AR-40

samtools sort 2004-AR-40.aligned.bam -o 2004-AR-40.sorted.bam samtools index 2004-AR-40.sorted.bam

That did create the files 2004-AR-40.aligned.bam, 2004-AR-40.aligned.stats, 2004-AR-40.sorted.bam, 2004-AR-40.sorted.bam.bai.

Here are my commands for the allele call:
../tools/lobSTR-bin-Linux-x86_64-4.0.6/bin/allelotype \ --command classify --bam 2004-AR-40.sorted.bam \ --noise_model ../tools/lobSTR-bin-Linux-x86_64-4.0.6/share/lobSTR/models/illumina_v3.pcrfree \ --out 2004-AR-40.sorted.bam --strinfo ./lobref/strinfo.tab \ --index-prefix ./lobref/lobSTR_

I get the following error:
[allelotype-4.0.6] 2020-04-21.16:30:21 ProgressMeter: Getting run info
terminate called after throwing an instance of std::out_of_range
what(): basic_string::substr: __pos (which is 18446744073709551166) > this->size() (which is 1130)
Aborted (core dumped)

It seems to be angry with the first contig in my obSTR_ref.fasta file, because it is 1131 bp in size?

Any help would be greatly appreciated!

[cnbdczsh]

Hello, may I ask, did you finally get it out? How is the bed file in the --str xx.bed file generated?