i am trying to use p-orthomcl for my large sized genome (too large to use orthofinder due to lack of space in our server)
and it seems like p-orthomcl has a shell script of its own where i can only execute a certain step of the procedure.
porthomcl.sh [OPTIONS] CONTAINER_FOLDER options -n, --nameregx a regular expression to treat file names (default behaviour remove extention (.+)\..+) -f, --field ID Field in input Fasta Files (default=1) -t, --threads number of threads/processes to run (default=4) -s, --startat an integer indicating the first Step to run (default=1) -e, --endafter an integer indicating the last Step to run (default=8) --wait wait for keypress at every step
so i tried something like this to execute the fifth step only, without prior steps folders in the directory
sh porthomcl.sh -s 5 -e 5 bacteria
and it did not work, saying that
./porthomcl.sh: 33: ./porthomcl.sh: [[: not found ./porthomcl.sh: 1: cd: Illegal option -s Container folder: /disk7/08.youngseok/hgt/porthomcl/PorthoMCL-master ./porthomcl.sh: 80: ./porthomcl.sh: [[: not found ERROR: CONTAINER_FOLDER does not contain 1.compliantFasta ./porthomcl.sh: 87: ./porthomcl.sh: Bad substitution
can anyone please tell me how to only execute a certain step in p-orthomcl without any folder from prior steps?