Encountering problems while using SNAP models

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Encountering problems while using SNAP models

Sagnik Banerjee
Hello,

I am using MAKER3 to generate annotation for Saccharomyces cerevisiae. In round1 I used assembled transcripts and the run was completed successfully. In the next round, I supplied gene models trained using SNAP. I keep getting an error that cites a problem with line 540 at snap.pm

Can't locate object method "add_entry" via package "1" (perhaps you forgot to load "1"?) at /project/software/7/apps/maker3/3.01.03/bin/../lib/Widget/snap.pm line 540.

--> rank=15, hostname=ceres14-compute-54.scinet.local

ERROR: Failed while annotating transcripts

ERROR: Chunk failed at level:1, tier_type:4

FAILED CONTIG:II


The problem is somewhat similar to the one discussed in http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/2018-January/003150.html. I have attached the error file. I have tried executing the same previously but the run did not complete and the job was killed. I was inspecting the run closely and I found that MAKER3 stopped writing to the .error file after a few minutes. I am including the portion that was written to the .error file. I have attached the relevant files. 

Could you please look into this? 

Thank you.
Sagnik Banerjee
Graduate Research Assistant
Bioinformatics and Computational Biology
Department of Statistics
Dr. Carson Andorf's Lab
Agricultural Research Service (ARS) Research Participation Program
Oak Ridge Institute for Science and Education (ORISE)
437, Bessey Hall
Iowa State University

"The moment I have realized God sitting in the temple of every human body, the moment I stand in reverence before every human being and see God in him - that moment I am free from bondage, everything that binds vanishes, and I am free" - Swami Vivekananda

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maker_opts.ctl (6K) Download Attachment
sacce.hmm (62K) Download Attachment
Error (411K) Download Attachment
round1.gff (18M) Download Attachment
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Re: Encountering problems while using SNAP models

Sagnik Banerjee
Hello,

Could you find what's wrong with this?

Thank you.
Sagnik Banerjee
Graduate Research Assistant
Bioinformatics and Computational Biology
Department of Statistics
Dr. Carson Andorf's Lab
Agricultural Research Service (ARS) Research Participation Program
Oak Ridge Institute for Science and Education (ORISE)
437, Bessey Hall
Iowa State University

"The moment I have realized God sitting in the temple of every human body, the moment I stand in reverence before every human being and see God in him - that moment I am free from bondage, everything that binds vanishes, and I am free" - Swami Vivekananda


On Sun, Jun 14, 2020 at 7:32 AM Sagnik Banerjee <[hidden email]> wrote:
Hello,

I am using MAKER3 to generate annotation for Saccharomyces cerevisiae. In round1 I used assembled transcripts and the run was completed successfully. In the next round, I supplied gene models trained using SNAP. I keep getting an error that cites a problem with line 540 at snap.pm

Can't locate object method "add_entry" via package "1" (perhaps you forgot to load "1"?) at /project/software/7/apps/maker3/3.01.03/bin/../lib/Widget/snap.pm line 540.

--> rank=15, hostname=ceres14-compute-54.scinet.local

ERROR: Failed while annotating transcripts

ERROR: Chunk failed at level:1, tier_type:4

FAILED CONTIG:II


The problem is somewhat similar to the one discussed in http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/2018-January/003150.html. I have attached the error file. I have tried executing the same previously but the run did not complete and the job was killed. I was inspecting the run closely and I found that MAKER3 stopped writing to the .error file after a few minutes. I am including the portion that was written to the .error file. I have attached the relevant files. 

Could you please look into this? 

Thank you.
Sagnik Banerjee
Graduate Research Assistant
Bioinformatics and Computational Biology
Department of Statistics
Dr. Carson Andorf's Lab
Agricultural Research Service (ARS) Research Participation Program
Oak Ridge Institute for Science and Education (ORISE)
437, Bessey Hall
Iowa State University

"The moment I have realized God sitting in the temple of every human body, the moment I stand in reverence before every human being and see God in him - that moment I am free from bondage, everything that binds vanishes, and I am free" - Swami Vivekananda

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org