[maker-devel] 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*

ᐧ

On Sun, Jun 14, 2020 at 7:32 AM Sagnik Banerjee <sagnik at iastate.edu> 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*
> ᐧ
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20200625/325a52d3/attachment-0004.html>