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MAKER only running 1 task

Seth_m55
Hello,

I'm running a MAKER annotation on an ubuntu cluster and my top screen shows the following:

Tasks: 831 total,   3 running, 826 sleeping,   0 stopped,   1 zombie

and my maker run (on a screen) shows:

...
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:4 now processing 0
flattening protein clusters
prepare section files
merging blast reports...
flattening protein clusters
prepare section files
merging blast reports...
flattening protein clusters
prepare section files

Of the 826, the vast majority of them are maker and only one of the running tasks is maker.  Is this normal behaviour or has my maker run stopped processing?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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Re: MAKER only running 1 task

Carson Holt-2
It may be frozen, or if it is on the last contig it can be running a non-paralelizable step (very last cluster merging step for each contig is not paralelizable). So on a large contig the very last step can take a little while, and if there are no other contigs, then there is no work to give to other processes to keep them busy in the meantime. So everyone has to wait so they can all exit together once the last step is done. But as I said, this will only happen if you are on the last contig and it is large. Otherwise it is probably frozen somehow (look for any errors further up the log).

—Carson





On May 10, 2017, at 2:24 PM, Seth Munholland <[hidden email]> wrote:

Hello,

I'm running a MAKER annotation on an ubuntu cluster and my top screen shows the following:

Tasks: 831 total,   3 running, 826 sleeping,   0 stopped,   1 zombie

and my maker run (on a screen) shows:

...
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:4 now processing 0
flattening protein clusters
prepare section files
merging blast reports...
flattening protein clusters
prepare section files
merging blast reports...
flattening protein clusters
prepare section files

Of the 826, the vast majority of them are maker and only one of the running tasks is maker.  Is this normal behaviour or has my maker run stopped processing?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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