CARD RGI BWT issues [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped

Question

[laujihen]

The bug I'm having the same issue as previously posted by some users, is there a fix for this, or any solution for troubleshooting?

Many many lines of: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped

Then it shows:

[bam_sort_core] merging from 36 files and 12 in-memory blocks...

Followed by various lines, different content, but the same format of

WARNING 2024-06-29 02:57:34,837 : model with id : 3278, has few mapped reads to make consensus sequence skipping: 'Prevalence_Sequence_ID:2857|ID:3278|Name:Acinetobacter_baumannii_AbaQ|ARO:3004574'

I believe the process were then terminated as I saw some temporary files, and when I look into the source code, I think the program will prompt a "DONE" message if the run is complete. And I did not see the message, or I left out some option?

My Command

rgi bwt --read_one "${in_dir}/${read1}" --read_two "${in_dir}/${read2}" --output_file "${out_dir}/${prefix}" --local --include_wildcard --include_other_models --clean -n 12

CARD Version
CARD version: 3.2.9
wildCARD version: 4.0.2

RGI version
RGI v 6.0.3 (downgraded KMA to 1.3.4)

Desktop:

Ubuntu 20.04.6 LTS, 64GB RAM

Had anybody experience the same issue or Is there anything I did wrong?