Hello,
I have managed to run the annotate and qc functions in DRAM2, and I would like to use the output from this to run summarize. According to the manual (https://dramit.readthedocs.io/en/latest/params_doc.html#summarize-options), I would only need to provide annotations.tsv using the --annotations flag, with optional --rrnas and --trnas flags. The error that I am getting appears to complain something about missing parameters or files, but by the looks of it, I am not sure exactly what I am missing at this point. This is how I am trying to run the summarize now:
nextflow run ycsong/DRAM -r dev \
--summarize --visualize --traits\
--distill_topic default \
--use_dbcan --use_kofam --use_merops \
--annotations "${annot_out}/ANNOTATE/annotations.tsv" \
--rrnas "${annot_out}/ANNOTATE/collected_rrnas.tsv" \
--trnas "${annot_out}/ANNOTATE/collected_trnas.tsv" \
-profile apptainer \
--outdir "${distill_out}"
The annotations.tsv is a copied version of raw-annotations.tsv file that is generated from the annotate function. Your assistance here would be much appreciated. Thank you.
Hello,
I have managed to run the annotate and qc functions in DRAM2, and I would like to use the output from this to run summarize. According to the manual (https://dramit.readthedocs.io/en/latest/params_doc.html#summarize-options), I would only need to provide annotations.tsv using the --annotations flag, with optional --rrnas and --trnas flags. The error that I am getting appears to complain something about missing parameters or files, but by the looks of it, I am not sure exactly what I am missing at this point. This is how I am trying to run the summarize now:
The annotations.tsv is a copied version of raw-annotations.tsv file that is generated from the annotate function. Your assistance here would be much appreciated. Thank you.