porthomcl - executing only the certain step of procedures
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19 months ago
seok1213neo ▴ 20

hey!

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?

threading porthomcl orthomcl thread • 392 views
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