[maker-devel] maker 2.28 blastx error

[Carson Holt]

It's actually a little more complicated than that.  You are already using
BLAST+.  The sequence you are running on is apparently entirely masked, so
there is nothing there to align.  The error thrown by NCBI BLAST+ when this
happens (currently "Sequence contains no data ") has changed slightly over
time.  As a result it causes MAKER to fail where wublast doesn't because the
error it throws is still recognized, captured by MAKER, and ignored.  You
can probably ignore that contig, run with a different version of BLAST, or
put the attached files in the Š/maker/lib/Widget/ directory.  I fixed the
check for the current message, so it will ignore the error (as long as the
error is still going to STDERR and not STDOUT).

--Carson


From:  Barry Moore <barry.moore at genetics.utah.edu>
Date:  Monday, 10 June, 2013 1:13 PM
To:  <michel.moser at ips.unibe.ch>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker 2.28 blastx error

Hi Michel,

Yes wublast is the problem.  On current versions of maker the opts file
defaults to ncbi+, but older versions the opts file defaults to wublast.
Just edit you maker_bopts.ctl file to have the line:

blast_type=ncbi+

It seems like this option may have been in maker_opts.ctl in older files, so
if you don't find it in bopts then look in opts.

B

On Jun 10, 2013, at 7:03 AM, <michel.moser at ips.unibe.ch>
 wrote:

> 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/inser
> t-bac2_datastore
> 
> To access files for individual sequences use the datastore index:
> /home/moser/PHD/ANNOTATION/maker/BAC2/ginas-try/insert-bac2.maker.output/inser
> t-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/inser
> t-bac2_datastore/1D/F1/bac2%3A383-131865//theVoid.bac2%3A383-131865/0/bac2%3A3
> 83-131865.0.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
> 
> 
> 
> <test1.fasta><maker_bopts.ctl><maker_exe.ctl><maker_opts.ctl><protein.fasta><i
> nsert-bac2.fasta>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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