Trichoderma & P. vulgaris interaction
Things to do
Things done
Loogbook
- 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
Loogbook
- 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
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 -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.
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