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Unknown variable 'BWA' -- Make sure you didn't misspell it or define somewhere in the script before use it #24

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hhhhhywww opened this issue May 3, 2022 · 0 comments

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@hhhhhywww
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Hi
I am trying to use AMRplusplus for one of my metagenomics dataset. The software was installed in the cluster. However, when I tried to run the command, I have encountered the errors like unknow variables.
I have loaded bowtie2, java, nextflow before running the command.

nextflow run /share/apps/amrplusplus_v2-2.0.2/main_AmrPlusPlus_v2.nf --reads "path/*{1,2}P.fastq.gz" --adapters "/share/apps/amrplusplus_v2-2.0.2/data/adapters/nextera.fa" --host “path/_hostgenome_fasta.gz" --amr "/share/apps/amrplusplus_v2-2.0.2/data/amr/megares_modified_database_v2.00.fasta" --annotation "/share/apps/amrplusplus_v2-2.0.2/data/amr/megares_modified_annotations_v2.00.csv" --output "/ path /6-amrplusplus/output"

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