"command not found"

[lupolk]

Hi, I'm using WSL2 Ubuntu for Windows 10.

Ubuntu 22.04.3 LTS Windows 10 Version 10.0.19045.3803

I get the error below with all the methods I've tried. Downloading the geneidx release from Github with or without using a terminal and then running it, or using the first method given in "Running GeneidX example" in readme.

$ nextflow run ./main.nf -profile docker \
                                        --tsv /mnt/d/biotools-linux/geneidx/data/assemblies.tsv \
                                        --column_taxid_value GCA_905340225.1 \
                                        --column_path_value https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_905340225.1?download=true&gzip=true \
                                        --column_id_value 938171 \
                                        --outdir /mnt/d/biotools-linux/geneidx/output
[1] 543
--column_id_value: command not found
username@MSI:/mnt/d/biotools-linux/geneidx$ N E X T F L O W  ~  version 23.10.0
Launching `./main.nf` [curious_ride] DSL2 - revision: 2c57827f27

GENOMEMASKING+GENEID+BLASTx - NextflowPipeline
=============================================
output path: /mnt/d/biotools-linux/geneidx/output
tsv input path: /mnt/d/biotools-linux/geneidx/data/assemblies.tsv
id column: Assembly Accession
taxid column: GCA_905340225.1
path column: https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_905340225.1?download=true
mask genomes? false

After this the terminal is stuck (even after 3-4 hours) and there doesn't seem to be any activity until I type a random prompt, like s.

s
s: command not found

[1]+  Stopped                 nextflow run ./main.nf -profile docker --tsv /mnt/d/biotools-linux/geneidx/data/assemblies.tsv --column_taxid_value GCA_905340225.1 --column_path_value https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_905340225.1?download=true

I've tried excluding column_id_value command and this time it said command not found for outdir. I've excluded both and got a similar message again.

$ nextflow run ./main.nf -profile docker \
                                        --tsv /mnt/d/biotools-linux/geneidx/data/assemblies.tsv \
                                        --column_taxid_value GCA_905340225.1 \
                                        --column_path_value https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_905340225.1?download=true&gzip=true
[1] 874
username@MSI:/mnt/d/biotools-linux/geneidx$ N E X T F L O W  ~  version 23.10.0
Launching `./main.nf` [prickly_leavitt] DSL2 - revision: 2c57827f27

GENOMEMASKING+GENEID+BLASTx - NextflowPipeline
=============================================
output path: /mnt/d/biotools-linux/geneidx/output
tsv input path: /mnt/d/biotools-linux/geneidx/data/assemblies.tsv
id column: Assembly Accession
taxid column: GCA_905340225.1
path column: https://www.ebi.ac.uk/ena/browser/api/fasta/GCA_905340225.1?download=true
mask genomes? false

Then I have to do the same random typing to stop the process again, even though there is no activity, and I get the same "Stopped" message.

Edit: Confirmed it happens in v2.0.0 too.

[emiliorighi]

Hi, Thanks for using our pipeline. The command you are trying to launch is wrong. the parameters : column_taxid_value, column_path_value and column_id_value are the corresponding name of the columns of the tsv file you provide, as staten in the README. If you want to run the pipeline with the test assemblies you can just run:

nextflow run main.nf -profile docker

as if you take a look a the params.config file the column parameters are already mapped against the assemblies.tsv:

// Input options // mandatory tsv = "$projectDir/data/assemblies.tsv" // we could change this to NULL column_id_value = "Assembly Accession" column_path_value = "Path" column_taxid_value = "Organism Taxonomic ID"

Feel free to open another ticket if you are still having troubles running the pipeline