Hi,
thanks for the wonderful tool for long RNA reads analysis~

I am trying to run StringTie2 for rice ONT raw reads (fastq reads) by first running the uLTRA aligner (v0.0.4) and then provide generated sorted bam file to StringTie (v2.2.1). I have used IGV to check the bam file, it is ok.

Moreover, I have divided the bam file in different chromosomes to test, and I have found that the 90,001th~95,000th sorted reads cause "segmentation fault".

The bam file is here (5.8M) chr3_head90000_95000.bam.

The commands are as follow:

# ultra
uLTRA align $ref ${sample}.fq ${sample} --index ~/ricerna/ultra_bam/msu7_ultra_index --ont --t ${th} --prefix ${sample}_msu7 --use_NAM_seeds

# stringtie 
~/tool/stringtie-2.2.1.Linux_x86_64/stringtie -p 1 -L -l N1i1Chr3 -o chr3_head90000_95000.gtf chr3_head90000_95000.bam
#### Segmentation fault ####