For the segfault issue, it turn out to be the mismatch of fasts and gtf. I used the data from GENCODE rather than the data from AWS. The GENOMEGENERATE success. While another issue occurred, Error executing process > 'NFCORE_RNASEQRNASEQALIGN_STAR:STAR_ALIGN (AML4510)' Caused by: /home/eric777/my_rnaseq/work/7a/1ea95e4e94128f0f0feba30e5f0330/AML4510._STARpass1 Is shows exit 0, which means the ALIGN after ALIGN. There is no error code to check.