I am trying to assemble four relatively small bam files and getting a segmentation fault: 11 error. I can assemble two of them but the other two give this error. The last few lines of the -v output before the fault is

[02/07 15:54:55]>bundle GG704912:61240-61389 [6 alignments (4 distinct), 0 junctions, 0 guides] begins processing...
[02/07 15:54:55]^bundle GG704912:61240-61389 done (0 processed potential transcripts).
[02/07 15:55:10]>bundle GG704912:61822-4648378 [8800860 alignments (1931765 distinct), 9640 junctions, 0 guides] begins processing...
Segmentation fault: 11

I am using a Mac M1 64 GB with Ventura 13.1 - I have run stringtie before and not had this problem.

I see from others that they could find the problem in the bam file and eliminate it but I don't know how to do that.

Thanks

Theo Kirkland
UC San Diego
tkirkland@ucsd.edu