Argument order with wildcard data path

[malton-ont]

I am new...can someone help me to solve this error---Thank you (base) [mmolla@node304 ~]$ dorado basecaller /gpfs2/scratch/mmolla/Pod.pod5 dna_r10.4.1_e8.2_400bps_hac@v4.3.0 --modified-bases-models >/gpfs2/scratch/mmolla/HL3/calls.bam [2024-04-15 12:56:19.354] [info] Running: "basecaller" "/gpfs2/scratch/mmolla/Pod.pod5" "dna_r10.4.1_e8.2_400bps_hac@v4.3.0" "--modified-bases-models" [2024-04-15 12:56:19.400] [info] > Creating basecall pipeline [2024-04-15 12:56:19.414] [error] toml::parse: file open error -> /gpfs2/scratch/mmolla/Pod.pod5/config.toml (base) [mmolla@node304 ~]$ dorado basecaller /gpfs2/scratch/mmolla/Pod.pod5 dna_r10.4.1_e8.2_400bps_hac@v4.3.0 --modified-bases-models >/gpfs2/scratch/mmolla/HL3/calls.bam

Originally posted by @habibsaky in https://github.com/nanoporetech/dorado/issues/512#issuecomment-2057486471

[malton-ont]

Hi @habibsaky,

I've moved this to a new issue. The issue here looks to be down to the order of arguments interacting with the wildcard in your data path, and a missing argument for the modified bases model. Please try:

dorado basecaller \
    dna_r10.4.1_e8.2_400bps_hac@v4.3.0 \
    /gpfs2/scratch/mmolla/Pod*.pod5 \
    --modified-bases-model [path_to_modified_bases_model] \
> /gpfs2/scratch/mmolla/HL3/calls.bam

Note that if you want to process all the files in a directory you don't need the *.pod5, you can just pass the directory name as the argument.

[habibsaky]

Thank you . solve it.