Files involved are in /group/ctbrowngrp2/scratch/annie/2024-binning-kmer/sourmash_sig/
Trying to run as follows:
sourmash scripts mgsearch ERR3211994.abund.k15.contigs.single.sig.gz ERR3211994.abund.k15.reads.sig.gz -o ERR3211994.abund.csv
Where contigs.single.sig.gz is signature file of the genomes, and k15.reads.sig.gz is signature of the metagenome reads.
Getting the following error:
Traceback (most recent call last):
File "/home/amhorst/mambaforge/envs/branchwater/bin/sourmash", line 11, in
sys.exit(main())
File "/home/amhorst/mambaforge/envs/branchwater/lib/python3.10/site-packages/sourmash/main.py", line 19, in main
retval = mainmethod(args)
File "/home/amhorst/mambaforge/envs/branchwater/lib/python3.10/site-packages/sourmash_plugin_containment_search.py", line 68, in main
return mgsearch(args.query_genome, args.metagenomes,
File "/home/amhorst/mambaforge/envs/branchwater/lib/python3.10/site-packages/sourmash_plugin_containment_search.py", line 86, in mgsearch
query_ss = query_ss[0]
IndexError: list index out of range
ctb
commented
9 months ago
Files involved are in /group/ctbrowngrp2/scratch/annie/2024-binning-kmer/sourmash_sig/
Trying to run as follows: sourmash scripts mgsearch ERR3211994.abund.k15.contigs.single.sig.gz ERR3211994.abund.k15.reads.sig.gz -o ERR3211994.abund.csv
Where contigs.single.sig.gz is signature file of the genomes, and k15.reads.sig.gz is signature of the metagenome reads. Getting the following error:
Traceback (most recent call last): File "/home/amhorst/mambaforge/envs/branchwater/bin/sourmash", line 11, in
sys.exit(main())
File "/home/amhorst/mambaforge/envs/branchwater/lib/python3.10/site-packages/sourmash/main.py", line 19, in main
retval = mainmethod(args)
File "/home/amhorst/mambaforge/envs/branchwater/lib/python3.10/site-packages/sourmash_plugin_containment_search.py", line 68, in main
return mgsearch(args.query_genome, args.metagenomes,
File "/home/amhorst/mambaforge/envs/branchwater/lib/python3.10/site-packages/sourmash_plugin_containment_search.py", line 86, in mgsearch
query_ss = query_ss[0]
IndexError: list index out of range