Hello, this afternoon I've been having troubles with the cluster because sometimes the commands work and sometimes they don't. Like for example "basename", or any other command in a module, even when I've loaded it before, it says "command not found". Is there something wrong going on in the cluster?? I remember I had this problem in the past rigth before the cluster had to undergo maintenance.
Thanks in advance
Hello @jramirez ,
No maintenance planned. Everything is fine on the cluster from our point of view.
If a "command not found" error happens, it's often due to an error on the PATH or other environment variable.
Can you reproduce the error ? Could you provide us all the sequence of commands ?
Hello, thenks so much for the reply, today it's working for some reason. An exmaple of what was happening is that in a job I was using basename to go over the files of a folder, and I kept getting the same "command not found: basename". Then my way of testing what was going on was to run the part of the job that contained the "basename" using echo, like this:
for fastq in ./*_R1_001.fastq.gz
do
ID=basename -s _R1_001.fastq.gz $fastq
echo ${ID}
done
And with this, if I used it several times (the exact same lines), some times it worked , but sometimes it displayed the "command not found: basename"
Hello,
Sorry for the response time.
I guess something goes wrong with the PATH environment variable (maybe you or a script have change it when it goes wrong). I don't see another explanation. It should work.
If you can reproduce it, you could give us all the commands used before and after.
Note: not part of the problem, but I would recommend to use ${} notation and to always backquote variables (as describe for example here: Bash scripting best practices - sap1ens blog). Moreover, I would also recommand to use $(cmd) for command substitution (as opposed to backquotes).
So I would write:
fastq in $(ls ./*_R1_001.fastq.gz)
do
ID=$(basename -s _R1_001.fastq.gz "${fastq}")
echo "${ID}"
done
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