Test input and resulting files for the seven primary programs of the lsaBGC suite are provided here. This test data uses publicly available genomics data for the species C. kefirresidentii species complex gathered from GTDB (R202) / NCBI (with 5 additional genomes included from NCBI not featured in GTDB R202 release). For testing of metagenomic mining capabilities, we randomly downsampled one paired-end readset three different times (using different seeds) with seqtk. The metagenomic sample was part of the dataset described by Swaney et al. 2022 and chosen because it was estimated to feature a high-abundance of Corynebacterium.
To test each command please change-directory to the subdirectory and use bash to run the testing/example commmand (*.cmd). For more details on the inputs and outputs for each command tested, see the detailed walkthrough of typical workflows as well as the respective page for each of the seven core lsaBGC programs on the lsaBGC Wiki. Note, that input files listing paths to other files were edited to use local paths, but generally lsaBGC references global/full paths.
Each command is specified to use 4 cores/threads and time estimates are based on this. We ran tests on a server running Ubuntu 18.04.06 LTS with AMD EPYC 7451 24-Core processors.
lsaBGC-Ready.py (shows how to start off lsaBGC analysis using precomputed antiSMASH and BiG-SCAPE results)
# Noe, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-Ready/
bash test_lsaBGC-Ready.sh &> log.txtResults from the time function in Unix:
real 1m14.673s
user 3m6.711s
sys 0m18.213s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-Cluster/
bash test_lsaBGC-Cluster.sh &> log.txtResults from the time function in Unix:
real 0m1.089s
user 0m2.092s
sys 0m7.223s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated.
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-Refiner/
bash test_lsaBGC-Refiner.sh &> log.txtResults from the time function in Unix (also includes running lsaBGC-See twice to visualize before and after refinement results):
real 1m8.324s
user 1m6.226s
sys 1m0.170s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-Expansion/
bash test_lsaBGC-Expansion.sh &> log.txtResults from the time function in Unix:
real 0m42.674s
user 1m32.919s
sys 0m21.066s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-See/
bash test_lsaBGC-See.sh &> log.txtResults from the time function in Unix:
real 0m18.546s
user 0m15.443s
sys 0m7.711s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-PopGene/
bash test_lsaBGC-PopGene.sh &> log.txtResults from the time function in Unix:
real 6m50.525s
user 22m54.290s
sys 0m45.867s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-Divergence/
bash test_lsaBGC-Divergence.sh &> log.txtResults from the time function in Unix:
real 0m2.901s
user 0m6.332s
sys 0m8.915s
# Note, assumes you have lsaBGC properly installed
# and the conda environment activated
cd /path/to/lsaBGC_Ckefir_Testing_Cases/Test_lsaBGC-DiscoVary/
bash test_lsaBGC-DiscoVary.sh &> log.txtResults from the time function in Unix:
real 3m16.201s
user 8m46.107s
sys 0m36.554s