User:Jose Fabricio Lopez/Notebook/GEDF/2012/09/04

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Trichoderma & P. vulgaris interaction

Things to do

  • Pass seeds to soil

Things done

  • Seeds passed.


  • We are have not a designated place to our work, so, we are using greenhouse max ~28°C.
  • 20 seeds in total.
    • 10 inoculated
    • 10 free of Trichoderma.
  • We are going to measure biomass, true leaves, root size, some pathologies and number of beans per plant.

Intergenic sequences in T.atroviride

Things to do

  • Wait for a training set of T.atroviride.
  • Submit the test to prediction.
  • Results of prediction, compare predicted genes with FrozenGeneCatalog of T.atro.

Things done

  • Results of training.
  • Submitted. Finished.
  • Still runing BLAST


  • This is the result of the training.

Mon Sep 03 22:36:29 CEST 2012 - Message:

Details of your job:

Training job ID: +++++++++++++

Species name: Trichoderma_atroviride

Genome file: Trichoderma_atroviride_v2.fasta

cDNA file: 454Isotigs.fna

Training gene structure file: Tatroviridev2_FrozenGeneCatalog_20100319.gff

Tue Sep 04 05:27:27 CEST 2012 - Error Message:

An error occured while running the AUGUSTUS training job ++++++++++.

I think this could be owed to fram stop codon. As shows AutoAug.err 164460 times. ExonModel::processInternalExon: in-frame stop codon

ExonModel::processInternalExon: in-frame stop codon

ExonModel::processInternalExon: in-frame stop codon

ExonModel::processInternalExon: in-frame stop codon

  • For prediction

Tue Sep 04 20:16:05 CEST 2012 - Message:

Details of your job:

Prediction job ID: +++++++++

Parameter archive: parameters.tar.gz

Genome file: Trichoderma_atroviride_v2.fasta

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: true

Tue Sep 04 21:06:07 CEST 2012 - Message:

Your AUGUSTUS prediction job +++++++++ finished.

  • BLASTp input

./blastp -db TrichodermaAtrovirideV2.aa -evalue 1e-5 -num_alignments 3 -query /home/fabricio/Desktop/GeneSiftWholeTables.Standardized/Augustus/Agustus\ test\ results/augustus/augustus.aa -out /home/fabricio/Desktop/GeneSiftWholeTables.Standardized/Augustus/Agustus\ test\ results/augustus/BLASTTestAugustusVsTrichodremaFrozenGene.txt -word_size 7 Apparently this is too big.