main_AmrPlusPlus_v2_withRGI.nf

[XC-Zhai]

Hello, I am new user for Amr++, when I run the following (not using Singularity):
nextflow run "/mnt/raid5/xichuan/amrplusplus_v2/amr_test/amrplusplus_v2/main_AmrPlusPlus_v2_withRGI.nf" --card_db "/mnt/raid5/xichuan/amrplusplus_v2/card.json" --reads "/mnt/raid5/xichuan/*R{1,2}_001.fastq.gz" --output test_arm -w work_dir

I got the following error:

N E X T F L O W ~ version 21.04.1
Launching /mnt/raid5/xichuan/amrplusplus_v2/amr_test/amrplusplus_v2/main_AmrPlusPlus_v2_withRGI.nf [pensive_avogadro] - revision: 77e0805d3d
[- ] process > RunQC -
[- ] process > QCStats -
[- ] process > BuildHostIndex -
[- ] process > AlignReadsToHost -
[- ] process > RemoveHostDNA -
[- ] process > HostRemovalStats -
[- ] process > NonHostReads -
[- ] process > BuildAMRIndex -
[- ] process > AlignToAMR -
[- ] process > RunResistome -
[- ] process > ResistomeResults -
[- ] process > SamDedupRunResistome -
[- ] process > SamDedupResistomeResults -
[- ] process > RunRarefaction -
[- ] process > ExtractSNP -
[- ] process > RunRGI -
[- ] process > SNPconfirmation -
[- ] process > Confirmed_AMR_hits -
[- ] process > Confirmed_ResistomeResults -
[- ] process > ExtractDedupSNP -
[- ] process > RunDedupRGI -
[- ] process > DedupSNPconfirmation -
[- ] process > ConfirmDedupAMRHits -
[- ] process > DedupSNPConfirmed_ResistomeResults -
Error executing process > 'BuildHostIndex (chr21.fasta)'

Caused by:
Unknown variable 'BWA' -- Make sure it is not misspelt and defined somewhere in the script before using it

Source block:
"""
${BWA} index ${host}
"""

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

Best,
Xichuan

[TakacsBertalan]

Hi!
I ran into the same problem, for me changing "${BWA}" to simply "bwa" in the main_AmrPlusPlus_v2_withRGI.nf script solved the issue. Although this only works if bwa is added to your path.