[maker-devel] Strange error at blastn step

[Daniel Standage]

I have since installed Maker on a different machine and tried it out. The
test run completed successfully, but as I commenced with the full genome
annotation, I have noticed the following error popping up frequently.

formating database...
#--------- command -------------#
Widget::formater:
/N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in
/tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/N/u/dstandag/Mason/local/bin/blastx -db
/tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query
/tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000
-num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000
-num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis -out
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8.blastx
#-------------------------------#
deleted:-10 hits
formating database...
#--------- command -------------#
Widget::formater:
/N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in
/tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/N/u/dstandag/Mason/local/bin/blastx -db
/tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query
/tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000
-num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000
-num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis -out
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9.blastx
#-------------------------------#
deleted:-6 hits
WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta.
stop here:comp59088_c1_seq7
ERROR: Fasta index error

FATAL ERROR
ERROR: Failed while polishig ESTs!!

ERROR: Chunk failed at level 14
!!
FAILED CONTIG:scaffold_0




--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold_1
Length: 5805686
#---------------------------------------------------------------------


My first thought based on the message is that *blastdbcmd* could not find
the sequence in the database. I verified this was the case--I could not
extract sequence *comp59088_c1_seq7* from the database Maker had created
under /tmp. However, after removing the index files and re-running *
makeblastdb* with the *-parse_seqids* option set, *blastdbcmd* successfully
extracted the sequence.

I was initially happy with this finding, but upon closer inspection it
looks like Maker does not use *blastdbcmd* to extract sequences, but rather
its own internal code. Therefore I'm still not sure where the problem is
and how I might fix it. Any insights?

Thanks!

--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University



On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage
<daniel.standage at gmail.com>wrote:

> Greetings!
>
> I am doing a test run of my Maker setup on a new machine, annotating a
> pretty short contig (about 3kb). However, there seems to be a hiccup during
> the blastn stage. This is the terminal message.
>
> #--------- command -------------#
> Widget::blastn:
> /share/home/01854/standage/local/bin/blastn -db
> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Efasta.mpi.10.7
> -query /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0
> -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend 3
> -word_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp
> 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking true -show_gis
> -out
> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker.output/maker.bogus_datastore/scaffold_866/theVoid.scaff
> old_866/scaffold_866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ETrimmomatic%2Efasta.mpi.10.7.blastn
> #-------------------------------#
> deleted:0 hits
> ERROR:  Could not obtain lock to format database
>
>
> FATAL ERROR
>  ERROR: Failed while doing blastn of ESTs!!
>
> ERROR: Chunk failed at level 8
> !!
> FAILED CONTIG:scaffold_866
>
>
> Several blastn steps appeared to have completed successfully to this one
> failing. Any ideas what could be causing this?
>
> Thanks!
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
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