[maker-devel] maker run error

[Maria Joana F. B. A. Guimarães]

Hi 

I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error:

bioinf at linux-hdoc:~/Desktop/TEMP> maker

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore



To access files for individual sequences use the datastore index:

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log



STATUS: Now running MAKER...







--Next Contig--



#---------------------------------------------------------------------

Now starting the contig!!

SeqID: contig-dpp-500-500

Length: 32156

#---------------------------------------------------------------------





running  repeat masker.

#--------- command -------------#

Widget::RepeatMasker:

cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1

#-------------------------------#

processing output: 

cycle 1 

cycle 2 

cycle 3 

cycle 4 

cycle 5 

cycle 6 

cycle 7 

cycle 8 

cycle 9 

cycle 10 

Generating output... 

masking

done

formating database...

#--------- command -------------#

Widget::formater:

/home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0

#-------------------------------#

running  blast search.

#--------- command -------------#

Widget::blastx:

/home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner

#-------------------------------#

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

ERROR: BLASTX failed

ERROR: Failed while doing blastx repeats

ERROR: Chunk failed at level:1, tier_type:1

FAILED CONTIG:contig-dpp-500-500



ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:contig-dpp-500-500









--Next Contig--



Processing run.log file...

MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner

did not finish on the last run and must be erased

#---------------------------------------------------------------------

Now retrying the contig!!

SeqID: contig-dpp-500-500

Length: 32156

Tries: 2!!

#---------------------------------------------------------------------





re reading repeat masker report.

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out

running  blast search.

#--------- command -------------#

Widget::blastx:

/home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner

#-------------------------------#

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

ERROR: BLASTX failed

ERROR: Failed while doing blastx repeats

ERROR: Chunk failed at level:1, tier_type:1

FAILED CONTIG:contig-dpp-500-500



ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:contig-dpp-500-500









--Next Contig--



Processing run.log file...

MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner

did not finish on the last run and must be erased





Maker is now finished!!!



bioinf at linux-hdoc:~/Desktop/TEMP> 




Can you please help me?
Thanks

Joana
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