terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid

[ilariastewart]

Hi there,

I am running vamos as seen below (with file paths abbreviated)... I keep running into this "terminate" error. I cannot seem to find any documentation of this error online in regards to vamos. I have checked all file paths and formats and all seems good there.

module load vamos/1.2.2

vamos --read -b /mnt/scratch/*.bam -r /mnt/vntr_region_motifs.e.bed -s sample_name -o /mnt/scratch/*.vcf -t 8
option -input with `/mnt/scratch/*.bam'
option -region with `/mnt/vntr_region_motifs.e.bed '
option -sampleName with `sample_name'
option -output with `/mnt/scratch/*.vcf'
option -numThreads with `8'
locuswise_flag is set. 
finish reading 467078 vntrs
finish writing the header
start thread: 0
start thread: 1
start thread: 2
start thread: 3
start thread: 4
start thread: 5
start thread: 6
start thread: 7
terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_M_construct null not valid

Any help is much appreciated!!

[mchaisso]

Hi, can you try running the version 1.3.6? It is available in bioconda. THanks, -Mark

…

On Thu, Oct 26, 2023 at 11:50 AM ilariastewart ***@***.***> wrote: Hi there, I am running vamos as seen below (with file paths abbreviated)... I keep running into this "terminate" error. I cannot seem to find any documentation of this error online in regards to vamos. I have checked all file paths and formats and all seems good there. module load vamos/1.2.2 vamos --read -b /mnt/scratch/*.bam -r /mnt/vntr_region_motifs.e.bed -s sample_name -o /mnt/scratch/*.vcf -t 8 option -input with `/mnt/scratch/*.bam' option -region with `/mnt/vntr_region_motifs.e.bed ' option -sampleName with `sample_name' option -output with `/mnt/scratch/*.vcf' option -numThreads with `8' locuswise_flag is set. finish reading 467078 vntrs finish writing the header start thread: 0 start thread: 1 start thread: 2 start thread: 3 start thread: 4 start thread: 5 start thread: 6 start thread: 7 terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid Any help is much appreciated!! — Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKPGPUWHMDDXXEJT2RNYCDYBKWFVAVCNFSM6AAAAAA6RVTNBWVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3DIMJWHE4TANA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ilariastewart]

Hi Mark,

Thanks for your quick reply! This solved the problem.

Best,
Ilaria

[mchaisso]

Great, will close then.

[mchaisso]

Hi Ilaria,
Are you able to share the region with the error and/or the sequences you are running on? Also, the command should take in a single bam and produce a single vcf.

Thanks,
-Mark

[mchaisso]

Is this on a pacbio or nanopore bam? If you can share raw reads (overlapping only this region +/- about 50kb), can you send to my usc e-mail?

Thanks,
-Mark