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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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(ERR): hisat2-align died with signal 6 (ABRT) (core dumped) #396

Open dianzhiyong opened 2 years ago

dianzhiyong commented 2 years ago

hi,doctor i encounter a problem when use hisat2 ,can you give me some advice fisrt,i use hisat2 build index for a large genome : hisat2-build --large-index ,it doesn't report any error . then i map reads to index : hisat2 -x ${genome_index} -1 test_clean.1.fq.gz -2 test_clean.1.fq.gz -p 4 ,A faw minutes later, hisat2 report as below

terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc (ERR): hisat2-align died with signal 6 (ABRT) (core dumped)

thank you very much

SC-Duan commented 1 year ago

Hi, I got the same error, how did you work it out finally?

dianzhiyong commented 1 year ago

how long is the longest chromosome of the genome ？ may be it's because the chromosome is too long for my issue . you can try bowtie2

SC-Duan commented 1 year ago

It is about 2Gb. Thank you very much, I will try that.