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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>
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<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>
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<div>On May 28, 2013, at 7:37 PM, Jingjing Jin wrote:</div>
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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>
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