libc++abi: terminating in hisat-3n-table about hisat2 HOT 5 OPEN

Hello @hwlim ,

Thank you for using HISAT-3N. hisat-3n-table is designed for the HISAT-3N downstream analysis. Because hisat-3n-table requires some special tags that generated by hisat-3n, feeding hisat-3n-table with the SAM file generated by other software may cause error. Could you try hisat-3n for alignment step?

Best,
Leo

from hisat2.

Sorry, my question was not specific enough.
Actually, the input bam file was generated from hisat-3n in a linux system.
I wanted to try hisat-3n-table in my local mac machine and got the error.

• Lim

from hisat2.

@hwlim

Thank you for your response. Could you show me the exact script for your hisat-3n-table running and the full error message?

Thanks,
Leo

from hisat2.

That was just it:

hisat-3n-table --alignments align.bam --ref genome.fa --base-change C,T
ref pos strand convertedBaseQualities convertedBaseCount unconvertedBaseQualities unconvertedBaseCount
libc++abi: terminating
Abort trap: 6

from hisat2.

Hello @hwlim ,

Because hisat-3n-table only accept SAM file for --alignment input, it raise error. Please use samtools to convert the BAM to SAM, then use hisat-3n-table. Please see hisat-3n manual for more detail.

Best,
Leo

from hisat2.