Hello,
I’m constructing a little pipeline that combines bits of QIIME and Mothur, coming from trim.flows()…
source /macqiime/configs/bash_profile.txt
THEFILES=/Users/me/Documents/sffs/*.files
for f in $THEFILES
do
mothur "#shhh.flows(file=$f)" &
nrwait 8 #work with later
done
wait
function nrwait() {
local nrwait_my_arg
if [[ -z $1 ]] ; then
nrwait_my_arg=2
else
nrwait_my_arg=$1
fi
while [[ $(jobs -p | wc -l) -ge $nrwait_my_arg ]] ; do
sleep 0.33;
done
}
Basically, this little script (that is called from the main script) calls and runs n (upto 8 here) shhh.flows() in parallel.
Every time it finished processing a file..
Finalizing...
[ERROR]: Could not open /Users/me/Documents/sffs//Users/me/Documents/sffs/muhfile.shhh.fasta
[ERROR]: Could not open /Users/me/Documents/sffs//Users/me/Documents/sffs/muhfile.shhh.names
Total time to process /Users/me/Documents/sffs/muhfile.muhfile.flow: 5842 5837.61
Output File Names:
/Users/me/Documents/sffs/muhfile.muhfile.shhh.qual
/Users/me/Documents/sffs/muhfile.muhfile.shhh.fasta
/Users/me/Documents/sffs/muhfile.muhfile.shhh.names
/Users/me/Documents/sffs/muhfile.muhfile.shhh.counts
/Users/me/Documents/sffs/muhfile.muhfile.shhh.groups
/Users/me/Documents/sffs//Users/me/Documents/sffs/muhfile.shhh.fasta
/Users/me/Documents/sffs//Users/me/Documents/sffs/muhfile.shhh.names
Is it safe to ignore these error messages? I mean, are muhfile.muhfile.shhh.fasta and muhfile.muhfile.shhh.names the same files as muhfile.shhh.fasta and muhfile.shhh.names that it’s (for whatever reason) trying (and failing) to create to the clearly wrong path?