[W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped

[hazmup]

Hi, I'm running rgi bwt on some metagenomics data and when writing the bam file there seems to be some issue that produces millions of these errors which also cause it to take very long. The command I am running is this: rgi bwt --local --read_one R1 --read_two R2 --threads 16 --output_file ~/card/${baseName} --includewildcard --clean 2>/mnt/d/logs/card$(date +%s).err 1>/mnt/d/logs/card_$(date +%s).out

[atalgarni53860]

I have the same problem and the run is still working for 4 days now. the run can not proceed to produce output file it is fixed or somehow wandering btw mapping and sorting...

[PB-Shinde]

I am having the same issue, after the "mapped query cannot have zero coordinates; treated as unmapped" error it shows "merging from 0 files and 7 in-memory blocks" after this starts raising "WARNING :model with id : 128, has few mapped reads to make consensus sequence skipping : ARO:ID"

this warning returns with another ARO ID again and again for hundreds of times then the process kets killed.

please send solutions

[github-actions[bot]]

Issue is stale and will be closed in 7 days unless there is new activity

[JennKnapp]

I am running into the exact same issue, is there a fix for this, or any troubleshooting suggestions? command: rgi bwt --local --read_one R1.fastq.gz --read_two R2.fastq.gz --output_file ~/card_output/sample_name

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

Then it eventually shows: "merging from 0 files and 16 in-memory blocks" and then many lines of: "WARNING :model with id : 128, has few mapped reads to make consensus sequence skipping : ARO:ID"

the process is then terminated.