[maker-devel] maker 2.28 blastx error

[michel.moser at ips.unibe.ch]

Hello Maker-developper and user

I am using maker for the first time to annotate some BAC-sequences. 
I successfully run both of the test-data sets provided in the maker tarball but when i run maker on my
sequences and provide some EST-evidence from cufflinks, i get errors at repeat database blasting (see error below).
As te_protein data set i just use the provided file in maker/data/. 

I sent the data to a colleague which could run it without problem using maker2.10. 
Or is the problem that i dont have wublast and RepBase installed? 

Any hint is highly appreciated! 

Thanks, 
Michel


std.error

STATUS: Parsing control files...
WARNING: blast_type is set to 'wublast' but executables cannot be located
The blast_type 'ncbi+' will be used instead.

STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/moser/PHD/ANNOTATION/maker/BAC2/ginas-try/insert-bac2.maker.output/insert-bac2_datastore

To access files for individual sequences use the datastore index:
/home/moser/PHD/ANNOTATION/maker/BAC2/ginas-try/insert-bac2.maker.output/insert-bac2_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: bac2:383-131865
Length: 131482
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_rcBcxr/0/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_rcBcxr/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_rcBcxr/0/bac2%3A383-131865.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/moser/PHD/ANNOTATION/maker/BAC2/ginas-try/insert-bac2.maker.output/insert-bac2_datastore/1D/F1/bac2%3A383-131865//theVoid.bac2%3A383-131865/0/bac2%3A383-131865.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
BLAST engine error: Warning: Sequence contains no data 
BLAST engine error: Warning: Sequence contains no data 
ERROR: BLASTX failed
--> rank=NA, hostname=ipsktube
ERROR: Failed while doing blastx repeats
ERROR: Chunk failed at level:1, tier_type:1
FAILED CONTIG:bac2:383-131865

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:bac2:383-131865

examining contents of the fasta file and run log



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