[maker-devel] maker running error

[Mark Yandell]

Hi Jingjing,

looks like your fasta files have problems. Have you checked to see if they are formatted correctly?

cheers,

--mark

On May 28, 2013, at 7:37 PM, Jingjing Jin wrote:

Dear all,

When I try to run maker on my datasets, there is an error like this:

#--------- command -------------#
Widget::blastx:
/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
#-------------------------------#
[blastall] FATAL ERROR:  search cannot proceed due to errors in all contexts/frames of query sequences
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/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
#-------------------------------#
[blastall] FATAL ERROR:  search cannot proceed due to errors in all contexts/frames of query sequences
deleted:0 hits
running  blast search.

#--------- command -------------#
Widget::blastn:
/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
#-------------------------------#
[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
[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
ERROR: BLASTN failed

FATAL ERROR
ERROR: Failed while doing blastn of ESTs!!

ERROR: Chunk failed at level 8
!!
FAILED CONTIG:C4345703


Could anyone give me some suggestions?

Thanks!

Jingjing


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