[maker-devel] ERROR: Failed while gathering ab-init output files

[Jia-Xing Yue]

Hello,

I was trying to run maker (version 2.31.8) for a yeast genome (a
sacharymyceise species). However, I got the following error message:
...
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/yjx/Programs/augustus-3.1/bin/augustus --species=saccharomyces
--UTR=off /tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0.saccharomyces.augustus
#-------------------------------#
running  trnascan.
#--------- command -------------#
Widget::trnascan:
/home/yjx/local/bin/tRNAscan-SE -b -q
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.eukaryotic.trnascan
#-------------------------------#
running  snoscan.
#--------- command -------------#
Widget::snoscan:
/home/yjx/local/bin/snoscan /home/yjx/Programs/snoscan/Sc-all-snos.fa
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.Sc-all-snos%2Efa.snoscan
#-------------------------------#
gathering ab-init output files

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not specify a Query End or Query Begin
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::GenericHSP::_query_seq_feature
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:1525
STACK: Bio::Search::HSP::GenericHSP::query
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:956
STACK: Bio::Search::HSP::HSPI::start
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/HSPI.pm:503
STACK: PhatHit_utils::add_offset
/home/yjx/Programs/maker/bin/../lib/PhatHit_utils.pm:1462
STACK: GI::parse_abinit_file /home/yjx/Programs/maker/bin/../lib/GI.pm:1199
STACK: Process::MpiChunk::_go
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /home/yjx/Programs/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=octopus.itc.unipi.it
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chrI_pilon

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

examining contents of the fasta file and run log


For this run, I modified the maker_opts.ctl file to specify the genome
sequences, customed EST sequences and customed proteome sequences (all in
fasta format) for the annotation. My setting for gene prediction is as
follows:

#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=saccharomyces #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)
est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna=/home/yjx/Programs/snoscan/Sc-all-snos.fa #rRNA file to have
Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no


BTW: I've also test maker with the sample data provided with the maker
package (dpp_contig.fasta, dpp_est.fasta and dpp_protein.fasta) and it ran
fine.

Could you help me to figure out what is the cause of this problem? Thanks
in advance!

Best,
Jia-Xing
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