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Old 02-08-2018, 08:46 AM   #1
Junior Member
Location: US

Join Date: May 2013
Posts: 4
Default CAP3 cygwin doesn't work.

I'm trying to assemble FASTA sequences with CAP3 on Windows using Cygwin.
I have cap3.cygwin.tar from Cygwin works fine as far as I can tell.

cap3.exe appears to do nothing. No errors, no output. This is what happens when I run the example:

edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
$ ls
README  xyz  xyz.con  xyz.qual

edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
$ cat README
The command for running cap3 on data set xyz

   ../cap3   xyz  >  xyz.out &

edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
$ ../cap3 xyz > xyz.out &
[1] 5048

edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
[1]+  Exit 127                ../cap3 xyz > xyz.out

edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
$ cat xyz.out

edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
Bash returns exit code 127. Google tells me this means something is "not found". But I have no leads as to what that might be. Any ideas?
esiefker is offline   Reply With Quote
Old 02-13-2018, 11:10 AM   #2
Senior Member
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,317

"something" being "command". That is, "command not found". Could we see the result of:

ls ../cap3

If that exists, then try:

chmod +x ../cap3

prior to rerunning your command.
pmiguel is offline   Reply With Quote

cap3, cygwin

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