Hi, I'm teaching a class at SDSU to undergraduates who are interested in bioinformatics. As part of their final projects, some students are using rapsearch to look for proteins in Sequence Read Archive data sets. Many of them keep running into the same issue which goes roughly like this:
QueryFileName Input/SRA_datasets/ERR281336.fastq
Queries are nucleotide sequences in fastq format
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/bin/sh: line 9: 10903 Aborted rapsearch -q Input/SRA_datasets/$l.fastq -d Input/Proteins/all_proteins -o Input/RAP_Results/$l -p Input/RAP_Results/$l -z 4 -a T
It only happens on certain data sets but it happens consistently. The students are using Jetstream 'Medium' Instances with 6 cores and 16gb of RAM.
Hi, I'm teaching a class at SDSU to undergraduates who are interested in bioinformatics. As part of their final projects, some students are using rapsearch to look for proteins in Sequence Read Archive data sets. Many of them keep running into the same issue which goes roughly like this:
It only happens on certain data sets but it happens consistently. The students are using Jetstream 'Medium' Instances with 6 cores and 16gb of RAM.
Any ideas?