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Shell Programming and Scripting
Bash script jumping too quickly to the next command - crash
Post 302973383 by tremblayemilie9 on Tuesday 17th of May 2016 10:35:43 AM
05-17-2016
Bash script jumping too quickly to the next command - crash
Hi, (I am not too good in command-lines).
I am running a bash script and at some point my loop starts to run super quickly. Then, the steps after do not get processed and there is no further outpout generated. I tried with the sleep 20s option, as I thought some steps would get overlapped, but it did not solve the issue.
The last command line before it crashes is done with Mothur, and the following which is problematic is to generate a metadata for qiime commands. Although it is not in the qiime environment yet, so the dependencies should not be affected.
Also, When I run the script up to this specific step, then manually launch the next part of the script, no problem occurs.
What is going on here?
Thanks a lot
I am running a bash script and at some point my loop starts to run super quickly. Then, the steps after do not get processed and there is no further outpout generated. I tried with the sleep 20s option, as I thought some steps would get overlapped, but it did not solve the issue.
The last command line before it crashes is done with Mothur, and the following which is problematic is to generate a metadata for qiime commands. Although it is not in the qiime environment yet, so the dependencies should not be affected.
Also, When I run the script up to this specific step, then manually launch the next part of the script, no problem occurs.
What is going on here?
Thanks a lot
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