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<div><span></span><span style="background-color: rgba(0, 0, 0, 0);">Dear Maker developer Team,
<br>When I rerun maker using the first maker derived GFF3 files together with two newly generated evidence of Proteins and ESTs, I failed. I set the parameters in the maker_opt.ctl file like this:
<br>-------------------------------------
<br>genome=CSL.fasta
<br>maker_gff=CSL_1st_maker.gff;
<br>est_gff=osi_csl_maker.pasa_assemblies_Maker.gff3;
<br>protein_gff=CSL_wise.gff3;
<br>est2genome=1;
<br>protein2genome=1;
<br>other parameters with default.
<br>Then, I run maker via MPI. However, during the 2nd run, I failed. Below is the error message:
<br>-----------------------------------
<br>preparing ab-inits
<br>preparing ab-inits
<br>preparing ab-inits
<br>gathering ab-init output files
<br>gathering ab-init output files
<br>gathering ab-init output files
<br>gathering ab-init output files
<br>prepare section files
<br>Gathering GFF3 input into hits - chunk:0
<br>gathering ab-init output files
<br>gathering ab-init output files
<br>gathering ab-init output files
<br>gathering ab-init output files
<br>prepare section files
<br>Gathering GFF3 input into hits - chunk:0
<br>prepare section files
<br><font color="#ff0000">Died at /home/xiaenhua/SoftWare/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
<br>--> rank=6, hostname=localhost.localdomain
<br>ERROR: Failed while prepare section files
<br>ERROR: Chunk failed at level:12, tier_type:3
<br>FAILED CONTIG:scaffold3
<br>
<br>ERROR: Chunk failed at level:4, tier_type:0
<br>FAILED CONTIG:scaffold3
</font><br>
<br>Gathering GFF3 input into hits - chunk:0
<br>gathering ab-init output files
<br>prepare section files
<br>Gathering GFF3 input into hits - chunk:0
<br><font color="#ff0000">Died at /home/xiaenhua/SoftWare/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
<br>--> rank=8, hostname=localhost.localdomain
<br>ERROR: Failed while prepare section files
<br>ERROR: Chunk failed at level:12, tier_type:3
<br>FAILED CONTIG:scaffold5
</font><br>
<br>prepare section files
<br>ERROR: Chunk failed at level:4, tier_type:0
<br>FAILED CONTIG:scaffold5
<br>........................
<br>........................
<br>-------------------------------------- </span></div><div><span style="background-color: rgba(0, 0, 0, 0);">My protein evidence gff3 file looks like this:</span></div><div><span style="background-color: rgba(0, 0, 0, 0);">scaffold3 genewise match 1276842 1277727 . - . ID=GeneWise.45.m
<br>scaffold3 genewise match_part 1277687 1277727 . - . ID=GeneWise.45.cds_1;Parent=GeneWise.45.m <br>scaffold3 genewise match_part 1276842 1277545 . - . ID=GeneWise.45.cds_2;Parent=GeneWise.45.m</span></div><div><span style="background-color: rgba(0, 0, 0, 0);"><br></span></div><div><span style="background-color: rgba(0, 0, 0, 0);">EST evidence gff3:</span></div><div><span style="background-color: rgba(0, 0, 0, 0);">scaffold3 match 1275835 1276664 . + . ID=align_24718.m
<br>scaffold3 match_part 1275835 1276664 . + . ID=align_24718.cds_1;Parent=align_24718.m<br>scaffold3 match 2510415 2511782 . + . ID=align_24719.m
<br>scaffold3 match_part 2510415 2511782 . + . ID=align_24719.cds_1;Parent=align_24719.m<br>scaffold3 match 4113431 4114364 . + . ID=align_24720.m
<br>scaffold3 match_part 4113431 4114364 . + . ID=align_24720.cds_1;Parent=align_24720.m<br></span><span style="background-color: rgba(0, 0, 0, 0);"><br></span></div><div><span style="background-color: rgba(0, 0, 0, 0);">I don't know what happened? Your any help will be appreciated greatly!
<br>Thank you!
<br>
<br>All the best,
<br>En-Hua Xia</span></div>
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