[maker-devel] maker running error

[Carson Holt]

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+.

--Carson


From:  Mark Yandell <myandell at genetics.utah.edu>
Date:  Tuesday, 28 May, 2013 9:58 PM
To:  Jingjing Jin <jjin01 at mail.rockefeller.edu>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker running error

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_gapcl
> ose_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_gapcl
> ose_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_gapcl
> ose_datastore/CE/E6/C4345703//theVoid.C4345703/C4345703.0.all_ref%2Efasta.blas
> tn.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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