Apologies for the duplicate post. I have posted this question to github but not heard any response.
I am trying to use cudamapper to align long reads to the human reference, which works when outputting to PAF format. When I try to generate SAM or BAM output I get errors that end with:
[E::sam_hrecs_update_hashes] Duplicate entry “5” in sam header
print_sam: could not add header value
[E::sam_hrecs_update_hashes] Duplicate entry “5” in sam headerAborted (core dumped)
/opt/GenomeWorks-2021.02.2/bin/cudamapper PAG33026_pass_concat.fastq.gz ../hg19a.fa -B > cudamapper_2021_02_02_GM24385.bam