Closed JSSaini closed 1 year ago
Dear @JSSaini
Sorry for the late response.
To get available options you can run nextflow run metaGT -profile conda --help
. I'll add information to the README soon.
To provide assembled metagenomes the option is correct except you forgot a second dash: --genome
To provide RNA reads I suggest to use --rna_reads
option.
If you encounter more problems do not hesitate to contact and send me the error message.
All the best Andrey
Hi, I would like to align the list of metagenome-assembled genomes to merged-metatranscriptomics libraries. Please suggest a reasonable command to run MetaGT? I tried the following, but it complains about genome input, maybe because of absolute paths.
nextflow run /media/bioinfoteam/SCRATCH_1TB/jssaini_scratch/github/metaGT/metaGT m -genome '*/media/bioinfoteam/SCRATCH_1TB/jssaini_scratch/Aline_MAGs/Aline_JS_combo/All_MAGs_work_13_Feb/stag_bins/drep_results_90_10/dereplicated_genomes/bakta_derep_mags_results/MAGs_2.5k/*.fa' --transcriptome '*.fastq'
Unknown option: -genome -- Check the available commands and options and syntax with 'help'
And how to open help documentation? Thank you for your kind assistance.