ERROR: formatdb failed

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ERROR: formatdb failed

Megan
I recently updated to Maker 2.04.  I am getting a fatal error when it is trying to format NCBI's non-redundant protein database.  It says it "Cannot add sequence number 310942 (lcl|16039_/tmp/maker_YKPmof/old_nr%2Efa.mp) because it has zero-length" (see below).  Each time I try and rerun it, it gives the same error with a different sequence number and different lcl|number.  This same database worked fine with an older version of maker (1.?) and a different database works fine with MAKER 2.04.  Any suggestions?

Thanks.
Megan

#--------- command -------------#
Widget::formatdb:
/home/masupple/../../hpc-data/masupple/maker_pipeline/blast-2.2.24/bin/formatdb -p T -i /tmp/maker_YKPmof/old_nr%2Efa.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/home/masupple/../../hpc-data/masupple/maker_pipeline/blast-2.2.24/bin/blastall -p blastx -d /tmp/maker_YKPmof/old_nr%2Efa.mpi.10.1 -i /tmp/maker_YKPmof/rank0/Hera_D_Jan2010.0 -b 100000 -v
100000 -e 1e-06 -z 300 -Y 500000000 -a 1 -K 100 -U -F T -I -o /hpc-data/masupple/maker_pipeline/d_locus/Hera_D_Jan2010.maker.output/Hera_D_Jan2010_datastore/Hera_D_Jan2010/theVoid.Hera_D_Ja
n2010/Hera_D_Jan2010.0
.old_nr%2Efa.blastx.temp_dir/old_nr%2Efa.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formatdb:
/home/masupple/../../hpc-data/masupple/maker_pipeline/blast-2.2.24/bin/formatdb -p T -i /tmp/maker_YKPmof/old_nr%2Efa.mpi.10.2
#-------------------------------#
[formatdb] WARNING: Cannot add sequence number 310942 (lcl|16039_/tmp/maker_YKPmof/old_nr%2Efa.mp) because it has zero-length.

[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.
ERROR: formatdb failed

FATAL ERROR
ERROR: Failed while doing blastx of proteins!!

ERROR: Chunk failed at level 12
!!
FAILED CONTIG:Hera_D_Jan2010




     

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Re: ERROR: formatdb failed

Carson Hinton Holt
Re: [maker-devel] ERROR: formatdb failed Try deleting the mpi_blastdb directory and all it’s contents before running MAKER again, as it may just be a failed initialization step.  Also check that the drive storing your /tmp directory is not full.  The error is being thrown by NCBI BLAST itself.  It’s saying that on of the entries in the file is empty.  This can also be caused by bad formatted characters in the fasta file.

Try the following in a terminal window:

grep -P "[^\x09\x0A\x20-\x7F]" old_nr.fa

If there are any results then you have control character contamination of your input FASTA.

Thanks,
Carson


On 11/17/10 8:16 PM, "Megan" <hedgyx@...> wrote:

I recently updated to Maker 2.04.  I am getting a fatal error when it is trying to format NCBI's non-redundant protein database.  It says it "Cannot add sequence number 310942 (lcl|16039_/tmp/maker_YKPmof/old_nr%2Efa.mp) because it has zero-length" (see below).  Each time I try and rerun it, it gives the same error with a different sequence number and different lcl|number.  This same database worked fine with an older version of maker (1.?) and a different database works fine with MAKER 2.04.  Any suggestions?

Thanks.
Megan

#--------- command -------------#
Widget::formatdb:
/home/masupple/../../hpc-data/masupple/maker_pipeline/blast-2.2.24/bin/formatdb -p T -i /tmp/maker_YKPmof/old_nr%2Efa.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/home/masupple/../../hpc-data/masupple/maker_pipeline/blast-2.2.24/bin/blastall -p blastx -d /tmp/maker_YKPmof/old_nr%2Efa.mpi.10.1 -i /tmp/maker_YKPmof/rank0/Hera_D_Jan2010.0 -b 100000 -v
100000 -e 1e-06 -z 300 -Y 500000000 -a 1 -K 100 -U -F T -I -o /hpc-data/masupple/maker_pipeline/d_locus/Hera_D_Jan2010.maker.output/Hera_D_Jan2010_datastore/Hera_D_Jan2010/theVoid.Hera_D_Ja
n2010/Hera_D_Jan2010.0
.old_nr%2Efa.blastx.temp_dir/old_nr%2Efa.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formatdb:
/home/masupple/../../hpc-data/masupple/maker_pipeline/blast-2.2.24/bin/formatdb -p T -i /tmp/maker_YKPmof/old_nr%2Efa.mpi.10.2
#-------------------------------#
[formatdb] WARNING: Cannot add sequence number 310942 (lcl|16039_/tmp/maker_YKPmof/old_nr%2Efa.mp) because it has zero-length.

[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.
ERROR: formatdb failed

FATAL ERROR
ERROR: Failed while doing blastx of proteins!!

ERROR: Chunk failed at level 12
!!
FAILED CONTIG:Hera_D_Jan2010




     

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