I am using both short- and long-read-based BAM files in StringTie. However, the '-mix' mode resulted in an error message of 'Segmentation fault' as attached below. I have tried to just input alignments of either short reads or long reads individually. Both succeeded, which means only the '-mix' mode failed.
1- what could be the reason of the Segmentation fault?
2- could I try to use "stringtie merge" to merge separate long and short-read-based GTF files? Would this approach be comparable to the '-mix' mode?
Hi,
I am using both short- and long-read-based BAM files in StringTie. However, the '-mix' mode resulted in an error message of 'Segmentation fault' as attached below. I have tried to just input alignments of either short reads or long reads individually. Both succeeded, which means only the '-mix' mode failed.
1- what could be the reason of the Segmentation fault? 2- could I try to use "stringtie merge" to merge separate long and short-read-based GTF files? Would this approach be comparable to the '-mix' mode?
Thank you! Bohao
Error message below: /var/slurmd/spool/slurmd/job41897984/slurm_script: line 19: 232117 Segmentation fault (core dumped) /n/home00/bfang/programs/stringtie/stringtie --mix -o mix_reads.out.gtf $BAM_short_read longread_1234.bam -p 20 -v