Generation of core.xx file

[neptuneyt]

Dear developer, When I run the following command

$ cctyper test.fna out

the log as below seems Don't find any Cas operon,

[2024-10-07 20:41:21] INFO: Running CRISPRCasTyper version 1.8.0
[2024-10-07 20:41:21] INFO: Predicting ORFs with prodigal
[2024-10-07 20:41:34] INFO: Running HMMER against Cas profiles
100%|██████████| 705/705 [00:39<00:00, 17.93it/s]
[2024-10-07 20:42:15] INFO: Subtyping putative operons
[2024-10-07 20:42:16] INFO: Predicting CRISPR arrays with minced
[2024-10-07 20:42:17] INFO: BLASTing for CRISPR near cas operons
[2024-10-07 20:42:23] INFO: No CRISPRs found.
[2024-10-07 20:42:23] INFO: Removing temporary files

but a core file is produced incidentally, which seems to indicate that hmmsearch failed.

(cctyper) $ gdb  core.99897
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-120.el7
[New LWP 99897]
Core was generated by `hmmsearch --domtblout /Soil179'.
Program terminated with signal 11, Segmentation fault.
#0  0x000055f446ce65c9 in ?? ()
./core.99897" is a core file.
Please specify an executable to debug.

I'm confused if the software is crashing or if it's just not finding Cas.

[Russel88]

Looks like hmmsearch is crashing, but still producing output that cctyper thinks is complete. Hard to say what is going on. Maybe your fasta headers contain special characters or is not formatted correctly?