MAKER should supply other output as well to STDERR. If you were running with nohup this was likely captured in the file nohup.out. The output there would be very informative for me in seeing what would have went wrong. You could also upload your job to MWAS where I could then help you debug it. You would just need to let me know the job_id after submission. http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi Thanks, Carson On 11/8/10 2:50 PM, "Mark Yandell" <myandell@...> wrote:
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Dear Carson,
Thank you for the reply. I here attach the tail of nohup. Please have a look and let me know of the delay or how could I make MAKER to skip the erroneous sequences. Thank you
On Mon, Nov 8, 2010 at 6:32 PM, Carson Holt <[hidden email]> wrote:
-- Praveen K. Raj Kumar, Ph.D Student, Teaching Associate, Miami University, Oxford,OH,USA. Lab: 513-529-4270 Office : 513-529-4210 _______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org |
You may need to give me more of the output. Thanks, Carson On 11/8/10 6:09 PM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@...> wrote: Dear Carson, _______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org |
I extracted the lines corresponding to the erroneous sequence in the nohup.out. I attach this here.
On Mon, Nov 8, 2010 at 8:13 PM, Carson Holt <[hidden email]> wrote:
-- Praveen K. Raj Kumar, Ph.D Student, Teaching Associate, Miami University, Oxford,OH,USA. Lab: 513-529-4270 Office : 513-529-4210 _______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org |
In reply to this post by Carson Hinton Holt
![]() I’ve attached a handy perl script that will fix the file. USAGE: perl purify pita.cDNA-FLcDNA.fasta > pita.cDNA-FLcDNA_fixed.fasta After cleaning the file, you must reconfigure the control option files to use the new file. I would recommend clobbering all current control files using maker -CTL and then re-entering all options. This will make sure all options are updated to the current MAKER 2.04. You will also want to do a completely new run to destroy old files contaminated by the bad data as it will affect many analyses. Thanks, Carson On 11/10/10 11:54 AM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@...> wrote: Dear carson, ------ End of Forwarded Message _______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org |
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