No such option: -i

[mabouelk]

Usage: bigscape.py [OPTIONS] COMMAND [ARGS]...
Try 'bigscape.py -h' for help.

Error: No such option: -i
[Fri Jan 10 22:11:07 2025]
Error in rule bigscape_exe:
jobid: 33
input: intermediate_files/antismash/Pseudomonas_syringae_X00001_O/Pseudomonas_syringae_X00001_O.gbk, intermediate_files/antismash/Pseudomonas_syringae_X00002_O/Pseudomonas_syringae_X00002_O.gbk, intermediate_files/antismash/Pseudomonas_syringae_X00005_O/Pseudomonas_syringae_X00005_O.gbk, intermediate_files/antismash/Pseudomonas_syringae_X00004_O/Pseudomonas_syringae_X00004_O.gbk, intermediate_files/antismash/Pseudomonas_syringae_X00006_O/Pseudomonas_syringae_X00006_O.gbk, intermediate_files/antismash/Pseudomonas_syringae_X00007_O/Pseudomonas_syringae_X00007_O.gbk, intermediate_files/antismash/Pseudomonas_syringae_X00003_O/Pseudomonas_syringae_X00003_O.gbk, intermediate_files/PFAM/Pfam-A.hmm
output: intermediate_files/BiG-SCAPE/bigscape_output/index.html, intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal/mix/mix_clustering_c0.70.tsv, intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal/mix/mix_c0.70.network, intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal/Network_Annotations_Full.tsv
conda-env: bigscape_bacLIFE
shell:
python BiG-SCAPE/bigscape.py -i intermediate_files/antismash/ -o intermediate_files/BiG-SCAPE/bigscape_output/ --pfam_dir intermediate_files/PFAM/ --mode glocal --mibig --cutoffs 0.3 0.7 --include_singletons --cores 16 --mix; rm -r intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal; mv intermediate_files/BiG-SCAPE/bigscape_output/network_files/*hybrids_glocal intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[nlouwen]

Hi, it looks like you are trying to run the BiG-SCAPE version 2-beta with an outdated v1 command. With the update, we have made various changes to how BiG-SCAPE is ran, see the wiki for in-depth information.

A similar working version of your command might be:
python BiG-SCAPE/bigscape.py cluster -i intermediate_files/antismash/ -o intermediate_files/BiG-SCAPE/bigscape_output/ --pfam-path intermediate_files/PFAM/Pfam-A.hmm --alignment-mode glocal --mibig-version 3.1 --gcf-cutoffs 0.3,0.7 --include-singletons --cores 16 --mix

Be aware that the output folder structure is additionally changed (see wiki), so amendments to moving of desired input files for the steps in your pipeline are likely needed.