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<p>Hi,</p>
<p>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.<br>
Have you ever notice this before? Is this due to a misuse of Maker
of my own?<br>
Thank you in advance for your answer.<br>
<br>
<font size="-1" face="Courier New, Courier, monospace">est_gff
file<br>
1 Cufflinks match 6706 11762 3194.685322 -
. ID=1:CUFF.4.1;Name=1:CUFF.4.1;<br>
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 +;<br>
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 +;<br>
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 +;<br>
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 +;<br>
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 +;<br>
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 +;<br>
<br>
protein_gff file<br>
5 exonerate protein_match 8111679 8145811 .
- . ID=5:1;Target=ENSAMXP00000000017.1<br>
5 exonerate match 8111679 8111886 83.57 -
. ID=5:1:exon-1;Parent=5:1;Target=ENSAMXP00000000017.1 1 69<br>
5 exonerate match 8120294 8120428 83.57 -
. ID=5:1:exon-2;Parent=5:1;Target=ENSAMXP00000000017.1 70 84<br>
5 exonerate match 8125321 8125515 83.57 -
. ID=5:1:exon-3;Parent=5:1;Target=ENSAMXP00000000017.1 84 174<br>
5 exonerate match 8128007 8128240 83.57 -
. ID=5:1:exon-4;Parent=5:1;Target=ENSAMXP00000000017.1 175
252<br>
5 exonerate match 8138856 8139127 83.57 -
. ID=5:1:exon-5;Parent=5:1;Target=ENSAMXP00000000017.1 253
317<br>
<br>
maker_evm.log <br>
#-----Transcript weights<br>
evmtrans=10 #default weight for source unspecified est/alt_est
alignments<br>
evmtrans:blastn=0 #weight for blastn sourced alignments<br>
evmtrans:est2genome=10 #weight for est2genome sourced alignments<br>
evmtrans:tblastx=0 #weight for tblastx sourced alignments<br>
evmtrans:cdna2genome=7 #weight for cdna2genome sourced
alignments<br>
evmtrans:est_gff:cufflinks=30 #weight for est_gff:cufflinks
sourced alignments<br>
<br>
#-----Protein weights<br>
evmprot=10 #default weight for source unspecified protein
alignments<br>
evmprot:blastx=2 #weight for blastx sourced alignments<br>
evmprot:protein2genome=15 #weight for protein2genome sourced
alignments<br>
evmprot:protein_gff:exonerate=15 #weight for
protein_gff:exonerate sourced alignments<br>
<br>
#-----Abinitio Prediction weights<br>
evmab=10 #default weight for source unspecified ab initio
predictions<br>
evmab:snap=10 #weight for snap sourced predictions<br>
evmab:augustus=10 #weight for augustus sourced predictions<br>
evmab:fgenesh=10 #weight for fgenesh sourced predictions<br>
evmab:genemark=7 #weight for genemark sourced predictions<br>
evmab:pred_gff:augustus=10 #weight for pred_gff:augustus sourced
predictions</font><br>
<br>
</p>
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