[maker-devel] ERROR: Failed while prepare section files

[xiaenhua at gmail.com]

Dear Maker developer Team, 
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: 
------------------------------------- 
genome=CSL.fasta 
maker_gff=CSL_1st_maker.gff; 
est_gff=osi_csl_maker.pasa_assemblies_Maker.gff3; 
protein_gff=CSL_wise.gff3; 
est2genome=1; 
protein2genome=1; 
other parameters with default. 
Then, I run maker via MPI. However, during the 2nd run, I failed. Below is the error message: 
----------------------------------- 
preparing ab-inits 
preparing ab-inits 
preparing ab-inits 
gathering ab-init output files 
gathering ab-init output files 
gathering ab-init output files 
gathering ab-init output files 
prepare section files 
Gathering GFF3 input into hits - chunk:0 
gathering ab-init output files 
gathering ab-init output files 
gathering ab-init output files 
gathering ab-init output files 
prepare section files 
Gathering GFF3 input into hits - chunk:0 
prepare section files 
Died at /home/xiaenhua/SoftWare/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188. 
--> rank=6, hostname=localhost.localdomain 
ERROR: Failed while prepare section files 
ERROR: Chunk failed at level:12, tier_type:3 
FAILED CONTIG:scaffold3 

ERROR: Chunk failed at level:4, tier_type:0 
FAILED CONTIG:scaffold3 

Gathering GFF3 input into hits - chunk:0 
gathering ab-init output files 
prepare section files 
Gathering GFF3 input into hits - chunk:0 
Died at /home/xiaenhua/SoftWare/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188. 
--> rank=8, hostname=localhost.localdomain 
ERROR: Failed while prepare section files 
ERROR: Chunk failed at level:12, tier_type:3 
FAILED CONTIG:scaffold5 

prepare section files 
ERROR: Chunk failed at level:4, tier_type:0 
FAILED CONTIG:scaffold5 
........................ 
........................ 
-------------------------------------- 
My protein evidence gff3 file looks like this:
scaffold3 genewise match 1276842 1277727 . - . ID=GeneWise.45.m 
scaffold3 genewise match_part 1277687 1277727 . - . ID=GeneWise.45.cds_1;Parent=GeneWise.45.m 
scaffold3 genewise match_part 1276842 1277545 . - . ID=GeneWise.45.cds_2;Parent=GeneWise.45.m

EST evidence gff3:
scaffold3 match 1275835 1276664 . + . ID=align_24718.m 
scaffold3 match_part 1275835 1276664 . + . ID=align_24718.cds_1;Parent=align_24718.m
scaffold3 match 2510415 2511782 . + . ID=align_24719.m 
scaffold3 match_part 2510415 2511782 . + . ID=align_24719.cds_1;Parent=align_24719.m
scaffold3 match 4113431 4114364 . + . ID=align_24720.m 
scaffold3 match_part 4113431 4114364 . + . ID=align_24720.cds_1;Parent=align_24720.m

I don't know what happened? Your any help will be appreciated greatly! 
Thank you! 

All the best, 
En-Hua Xia
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