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

[Carson Holt]

Could you rerun with the latest MAKER release, just to make sure that it stil happens with the current release (Version 2.31.7).  Run with 'maker -a’.  If it still happenes, then send me the GFF3 files you are using as input, and I’ll take a look.  Basically it’s happening because you are missing a start or end position for a feature in one of the files.

—Carson



> On Nov 19, 2014, at 5:47 AM, xiaenhua at gmail.com wrote:
> 
> 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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