<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>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 …/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).</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Barry Moore <<a href="mailto:barry.moore@genetics.utah.edu">barry.moore@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, 10 June, 2013 1:13 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:michel.moser@ips.unibe.ch">michel.moser@ips.unibe.ch</a>><br><span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] maker 2.28 blastx error<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Michel,<div><br></div><div>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:</div><div><br></div><div>blast_type=ncbi+</div><div><br></div><div>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.</div><div><br></div><div>B<br><div><div><br></div><div>On Jun 10, 2013, at 7:03 AM, <<a href="mailto:michel.moser@ips.unibe.ch">michel.moser@ips.unibe.ch</a>></div><div> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello Maker-developper and user<br><br>I am using maker for the first time to annotate some BAC-sequences. <br>I successfully run both of the test-data sets provided in the maker tarball but when i run maker on my<br>sequences and provide some EST-evidence from cufflinks, i get errors at repeat database blasting (see error below).<br>As te_protein data set i just use the provided file in maker/data/. <br><br>I sent the data to a colleague which could run it without problem using maker2.10. <br>Or is the problem that i dont have wublast and RepBase installed? <br><br>Any hint is highly appreciated! <br><br>Thanks, <br>Michel<br><br><br>std.error<br><br>STATUS: Parsing control files...<br>WARNING: blast_type is set to 'wublast' but executables cannot be located<br>The blast_type 'ncbi+' will be used instead.<br><br>STATUS: Processing and indexing input FASTA files...<br>STATUS: Setting up database for any GFF3 input...<br>A data structure will be created for you at:<br>/home/moser/PHD/ANNOTATION/maker/BAC2/ginas-try/insert-bac2.maker.output/insert-bac2_datastore<br><br>To access files for individual sequences use the datastore index:<br>/home/moser/PHD/ANNOTATION/maker/BAC2/ginas-try/insert-bac2.maker.output/insert-bac2_master_datastore_index.log<br><br>STATUS: Now running MAKER...<br>examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: bac2:383-131865<br>Length: 131482<br>#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br>doing blastx repeats<br>formating database...<br>#--------- command -------------#<br>Widget::formater:<br>/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_rcBcxr/0/blastprep/te_proteins%2Efasta.mpi.10.0<br>#-------------------------------#<br>running blast search.<br>#--------- command -------------#<br>Widget::blastx:<br>/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<br>#-------------------------------#<br>BLAST engine error: Warning: Sequence contains no data <br>BLAST engine error: Warning: Sequence contains no data <br>ERROR: BLASTX failed<br>--> rank=NA, hostname=ipsktube<br>ERROR: Failed while doing blastx repeats<br>ERROR: Chunk failed at level:1, tier_type:1<br>FAILED CONTIG:bac2:383-131865<br><br>ERROR: Chunk failed at level:2, tier_type:0<br>FAILED CONTIG:bac2:383-131865<br><br>examining contents of the fasta file and run log<br><br><br><br><span><test1.fasta></span><span><maker_bopts.ctl></span><span><maker_exe.ctl></span><span><maker_opts.ctl></span><span><protein.fasta></span><span><insert-bac2.fasta></span>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></div></blockquote></div><br><div apple-content-edited="true"><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div><br class="Apple-interchange-newline"></div><br></div></div></div>_______________________________________________
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