Hi,
My hisat2 runs were working all of yesterday and i'm running the same code with different files from the same experiment and now am getting segmentation faults after my runs. It gives me all of the alignment stats but then a line that says "Segmentation fault (core dumped)."
I'm even gettin the error (Segmentation fault (core dumped)) when I run hisat2 --version (after it tells me the version is 2.2.2 and the details of the build/compilation).
The code I'm running is as follows hisat2 -x genome -1 S36_repaired_R1.fastq -2 S36_repaired_R2.fastq -U S36_singletons.fastq -S S36_aligned.sam
I took the resulting file and ran it through samtools view -S -b S36_aligned.sam > S26_aligned.bam and then ran a samtools quickcheck -vvv S26_aligned.bam and got the below output (see image), which is consistent with a run with no Segfault.
Is this usable and should i just ignore the segmentation fault?
Hi,
My hisat2 runs were working all of yesterday and i'm running the same code with different files from the same experiment and now am getting segmentation faults after my runs. It gives me all of the alignment stats but then a line that says "Segmentation fault (core dumped)."
I'm even gettin the error (Segmentation fault (core dumped)) when I run hisat2 --version (after it tells me the version is 2.2.2 and the details of the build/compilation).
The code I'm running is as follows hisat2 -x genome -1 S36_repaired_R1.fastq -2 S36_repaired_R2.fastq -U S36_singletons.fastq -S S36_aligned.sam
I took the resulting file and ran it through samtools view -S -b S36_aligned.sam > S26_aligned.bam and then ran a samtools quickcheck -vvv S26_aligned.bam and got the below output (see image), which is consistent with a run with no Segfault.
Is this usable and should i just ignore the segmentation fault?