Unbound variable (line 253)

[iwilkie]

Hi,

I'm trying to run genome updater on a mac (macOS Monterey v12.6.3), I've run into some issues which were previously described and ran the troubleshooting steps (e.g. installing xargs and coreutils). I thought I got it running, but I ran into an issue that I haven't found described before:

bash-5.2$ ~/genome_updater.sh -T 'f__Akkermansiaceae' -M 'gtdb' -t '5' -o 'GTDB_Akkermansiaceae_May2024' -g 'bacteria' -f 'genomic.fna.gz' -d 'genbank,refseq'
-------------------------------------------
┌─┐┌─┐┌┐┌┌─┐┌┬┐┌─┐    ┬ ┬┌─┐┌┬┐┌─┐┌┬┐┌─┐┬─┐
│ ┬├┤ ││││ ││││├┤     │ │├─┘ ││├─┤ │ ├┤ ├┬┘
└─┘└─┘┘└┘└─┘┴ ┴└─┘────└─┘┴  ─┴┘┴ ┴ ┴ └─┘┴└─
                                     v0.6.3 
-------------------------------------------
Mode: NEW 
Args: -T 'f__Akkermansiaceae' -M 'gtdb' -t '5' -o 'GTDB_Akkermansiaceae_May2024' -g 'bacteria' -f 'genomic.fna.gz' -d 'genbank,refseq'
Outp: /Users/Isa/Downloads/GTDB_Akkermansiaceae_May2024/
-------------------------------------
Downloading assembly summary [2024-05-03_21-57-32]
 - Database [genbank,refseq]
 - Organism group [bacteria]
 -  assembly entries available

Filtering assembly summary [2024-05-03_21-57-32]
/Users/Isa/genome_updater.sh: line 253: 2: unbound variable

This is the line which is throwing the error:

bash-5.2$ sed '253q;d' ~/genome_updater.sh
    filtered_lines=${2}

No files were downloaded, and the log doesn't provide more details:

--- genome_updater version: 0.6.3 ---
Mode: NEW 
Args: -T 'f__Akkermansiaceae' -M 'gtdb' -t '5' -o 'GTDB_Akkermansiaceae_May2024' -g 'bacteria' -f 'genomic.fna.gz' -d 'genbank,refseq'
Outp: /Users/Isa/Downloads/GTDB_Akkermansiaceae_May2024/
-------------------------------------
Downloading assembly summary [2024-05-03_21-57-32]
 - Database [genbank,refseq]
 - Organism group [bacteria]
 -  assembly entries available

Filtering assembly summary [2024-05-03_21-57-32]

I'm wondering if this issue stems from me working from a mac. Have you encountered this issue before? If yes, is there any workaround or is it not possible because I'm trying to run from a mac?

Thanks,
Isa