I was able to run all these commands with a small subset .gfa file. However, while using the large .gfa file, I got an error:
/tmp/slurmd/job/slurm_script: line 16: Killed vg index -x output_1.xg -g output_1.gcsa -k 16 output_1.vg
terminate called after throwing an instance of 'std::runtime_error'
what(): Need XG, GCSA, and LCP to create a Mapper
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
I am looking for solutions for this error to create an index and downstream files. Thank you for any help!