<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>Yes, most likely an input fasta error. If that is not the case there are also some versions of BLAST that have version specific failures, and are fixed by upgrading blast. For example, I see you are using blastall which is from the older NCBI BLAST as apposed to the newer BLAST+.</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> Mark Yandell <<a href="mailto:myandell@genetics.utah.edu">myandell@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 28 May, 2013 9:58 PM<br><span style="font-weight:bold">To: </span> Jingjing Jin <<a href="mailto:jjin01@mail.rockefeller.edu">jjin01@mail.rockefeller.edu</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<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 running error<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><base href="x-msg://26/"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi <span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Jingjing,</span><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;">looks like your fasta files have problems. Have you checked to see if they are formatted correctly?</span></font></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;">cheers,</span></font></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;">--mark</span></font></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font><div><div>On May 28, 2013, at 7:37 PM, Jingjing Jin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; ">
Dear all,<br><br>
When I try to run maker on my datasets, there is an error like this:<br><br>
#--------- command -------------#<br>
Widget::blastx:<br>
/usr/local/bin/blastall -p blastx -d /tmp/maker_W3xpXQ/te_proteins%2Efasta.mpi.10.5 -i /tmp/maker_W3xpXQ/rank0/C4345703.0 -b 100000 -v 100000 -e 1e-06 -z 300 -Y 500000000 -a 1 -U -F T -I T -o /data/project/oil_palm/evolution/TS1/maker/TS1_gapclose.maker.output/TS1_gapclose_datastore/CE/E6/C4345703//theVoid.C4345703/C4345703.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner<br>
#-------------------------------#<br>
[blastall] FATAL ERROR: search cannot proceed due to errors in all contexts/frames of query sequences<br>
deleted:0 hits<br>
running blast search.<br>
#--------- command -------------#<br>
Widget::blastx:<br>
/usr/local/bin/blastall -p blastx -d /tmp/maker_W3xpXQ/te_proteins%2Efasta.mpi.10.6 -i /tmp/maker_W3xpXQ/rank0/C4345703.0 -b 100000 -v 100000 -e 1e-06 -z 300 -Y 500000000 -a 1 -U -F T -I T -o /data/project/oil_palm/evolution/TS1/maker/TS1_gapclose.maker.output/TS1_gapclose_datastore/CE/E6/C4345703//theVoid.C4345703/C4345703.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner<br>
#-------------------------------#<br>
[blastall] FATAL ERROR: search cannot proceed due to errors in all contexts/frames of query sequences<br>
deleted:0 hits<br>
running blast search.<br><br>
#--------- command -------------#<br>
Widget::blastn:<br>
/usr/local/bin/blastall -p blastn -d /tmp/maker_W3xpXQ/all_ref%2Efasta.mpi.10.0 -i /tmp/maker_W3xpXQ/rank0/C4345703.0 -b 100000 -v 100000 -e 1e-10 -E 3 -W 15 -r 1 -q -3 -G 3 -z 1000 -Y 500000000 -a 1 -U -F T -I T -o /data/project/oil_palm/evolution/TS1/maker/TS1_gapclose.maker.output/TS1_gapclose_datastore/CE/E6/C4345703//theVoid.C4345703/C4345703.0.all_ref%2Efasta.blastn.temp_dir/all_ref%2Efasta.mpi.10.0.blastn<br>
#-------------------------------#<br>
[blastall] WARNING: C4345703: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options<br>
[blastall] WARNING: C4345703: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options<br>
ERROR: BLASTN failed<br><br>
FATAL ERROR<br>
ERROR: Failed while doing blastn of ESTs!!<br><br>
ERROR: Chunk failed at level 8<br>
!!<br>
FAILED CONTIG:C4345703<br><br><br>
Could anyone give me some suggestions?<br><br>
Thanks!<br><br>
Jingjing<br><br><br></div>
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