Trouble with EVM and evidence from external GFF3

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Trouble with EVM and evidence from external GFF3

Cédric Cabau

Hi,

I use Maker 3.01.02-beta in mpi mode to merge data from gene models and cdna/protein evidence. I run Maker with entries est_gff, protein_gff and pred_gff in run_evm=1, est2genome=0 and protein2genome=0 mode. Being surprised by the amount of RAM required for some EVM jobs, I wanted to reproduce the execution of EVM commands outside of Maker. I commented the line 1819 inside maker/lib/GI.pm to keep the EVM command input files inside my temporary directory. By doing this, I noticed that the *.protein_for_evm.gff files generated for each chunk were systematically empty (only the gff3 header is written in the file) unlike the *.ests_for_evm.gff and *.preds_for_evm_gene.gff files. The formatting of my protein_gff input file does not seem to cause this because I find protein evidence in my output file *.all.maker.gff. Evidence files are therefore well taken into account by Maker but the protein evidence does not seem to have been passed on to EVM.
Have you ever notice this before? Is this due to a misuse of Maker of my own?
Thank you in advance for your answer.

est_gff file
1    Cufflinks    match    6706    11762    3194.685322    -    .    ID=1:CUFF.4.1;Name=1:CUFF.4.1;
1    Cufflinks    match_part    6706    6760    3194.685322    -    .    ID=1:CUFF.4.1:exon-1;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 1 55 +;
1    Cufflinks    match_part    6892    6955    3194.685322    -    .    ID=1:CUFF.4.1:exon-2;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 56 119 +;
1    Cufflinks    match_part    9558    9694    3194.685322    -    .    ID=1:CUFF.4.1:exon-3;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 120 256 +;
1    Cufflinks    match_part    10081    10191    3194.685322    -    .    ID=1:CUFF.4.1:exon-4;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 257 367 +;
1    Cufflinks    match_part    11550    11625    3194.685322    -    .    ID=1:CUFF.4.1:exon-5;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 368 443 +;
1    Cufflinks    match_part    11751    11762    3194.685322    -    .    ID=1:CUFF.4.1:exon-6;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 444 455 +;

protein_gff file
5    exonerate    protein_match    8111679    8145811    .    -    .    ID=5:1;Target=ENSAMXP00000000017.1
5    exonerate    match    8111679    8111886    83.57    -    .    ID=5:1:exon-1;Parent=5:1;Target=ENSAMXP00000000017.1 1 69
5    exonerate    match    8120294    8120428    83.57    -    .    ID=5:1:exon-2;Parent=5:1;Target=ENSAMXP00000000017.1 70 84
5    exonerate    match    8125321    8125515    83.57    -    .    ID=5:1:exon-3;Parent=5:1;Target=ENSAMXP00000000017.1 84 174
5    exonerate    match    8128007    8128240    83.57    -    .    ID=5:1:exon-4;Parent=5:1;Target=ENSAMXP00000000017.1 175 252
5    exonerate    match    8138856    8139127    83.57    -    .    ID=5:1:exon-5;Parent=5:1;Target=ENSAMXP00000000017.1 253 317

maker_evm.log
#-----Transcript weights
evmtrans=10 #default weight for source unspecified est/alt_est alignments
evmtrans:blastn=0 #weight for blastn sourced alignments
evmtrans:est2genome=10 #weight for est2genome sourced alignments
evmtrans:tblastx=0 #weight for tblastx sourced alignments
evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments
evmtrans:est_gff:cufflinks=30 #weight for est_gff:cufflinks sourced alignments

#-----Protein weights
evmprot=10 #default weight for source unspecified protein alignments
evmprot:blastx=2 #weight for blastx sourced alignments
evmprot:protein2genome=15 #weight for protein2genome sourced alignments
evmprot:protein_gff:exonerate=15 #weight for protein_gff:exonerate sourced alignments

#-----Abinitio Prediction weights
evmab=10 #default weight for source unspecified ab initio predictions
evmab:snap=10 #weight for snap sourced predictions
evmab:augustus=10 #weight for augustus sourced predictions
evmab:fgenesh=10 #weight for fgenesh sourced predictions
evmab:genemark=7 #weight for genemark sourced predictions
evmab:pred_gff:augustus=10 #weight for pred_gff:augustus sourced predictions



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