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BUG: split read ins!

See original GitHub issue

Hi Fritz,

I am trying to run a job on a large genome (2.8Gb). This is the consensus of a ighly heterozygous genome, so there should be a fair amount of heterozygous SV. I am getting an error in the first contig (42 thousand contigs in total). The command line was as follows:

sniffles -z 3 -d 10000 -t 26 -n -1 --report_BND --genotype --cluster --min_het_af 0.2 -m inia601.bam -v inia601.vcf
Estimating parameter...
        Max dist between aln events: 4
        Max diff in window: 50
        Min score ratio: 2
        Avg DEL ratio: 0.0315592
        Avg INS ratio: 0.154157
Start parsing... ctg1
BUG: split read ins! 6123 2852 m54329U_200324_174744/150668912/36192_62717
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
/var/spool/slurm/job4679576/slurm_script: line 38: 32633 Aborted                 (core dumped) sniffles -z 3 -d 10000 -t 26 -n -1 --report_BND --genotype --cluster --min_het_af 0.2 -m $bam -v inia601.vcf

I was trying to look for similar errors in this page, but they all seem to be at least half a year old and none related to any of the flags used for this run. could you perhaps point me in the right direction, what could be going wrong here?

Cheers,

Juan D. Montenegro

Issue Analytics

State:
Created 3 years ago
Comments:21 (10 by maintainers)

Top GitHub Comments

1reaction

yusmiatiliaucommented, Jun 16, 2020

Hi,

I got a similar error trying to run sniffles on one human genome nanopore data (11 Gb), mapped using minimap2.

sniffles -m /bam file/ -v /vcf file/ -s 2 -t 4 resulted in this error:

Estimating parameter… Max dist between aln events: 9 Max diff in window: 50 Min score ratio: 2 Avg DEL ratio: 0.0388139 Avg INS ratio: 0.0288268 Start parsing… chr1 BUG: split read ins! 9159 5855 a472e554-5071-4459-861a-93c9aa8f9ce8 terminate called after throwing an instance of ‘std::out_of_range’ what(): basic_string::substr: __pos (which is 8249) > this->size() (which is 5855) Aborted (core dumped)

will be thankful if you can advise what should I do to overcome the error?

Thanks

0reactions

fritzsedlazeckcommented, Feb 8, 2022

We just pushed a completely new version of Sniffles (v2.0.0.2) and hope this will be resolved.

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