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<P><FONT SIZE=2>Hi<BR>
<BR>
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:<BR>
<BR>
bioinf@linux-hdoc:~/Desktop/TEMP> maker<BR>
<BR>
STATUS: Parsing control files...<BR>
<BR>
STATUS: Processing and indexing input FASTA files...<BR>
<BR>
STATUS: Setting up database for any GFF3 input...<BR>
<BR>
A data structure will be created for you at:<BR>
<BR>
/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore<BR>
<BR>
<BR>
<BR>
To access files for individual sequences use the datastore index:<BR>
<BR>
/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log<BR>
<BR>
<BR>
<BR>
STATUS: Now running MAKER...<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
--Next Contig--<BR>
<BR>
<BR>
<BR>
#---------------------------------------------------------------------<BR>
<BR>
Now starting the contig!!<BR>
<BR>
SeqID: contig-dpp-500-500<BR>
<BR>
Length: 32156<BR>
<BR>
#---------------------------------------------------------------------<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
running repeat masker.<BR>
<BR>
#--------- command -------------#<BR>
<BR>
Widget::RepeatMasker:<BR>
<BR>
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<BR>
<BR>
#-------------------------------#<BR>
<BR>
processing output:<BR>
<BR>
cycle 1<BR>
<BR>
cycle 2<BR>
<BR>
cycle 3<BR>
<BR>
cycle 4<BR>
<BR>
cycle 5<BR>
<BR>
cycle 6<BR>
<BR>
cycle 7<BR>
<BR>
cycle 8<BR>
<BR>
cycle 9<BR>
<BR>
cycle 10<BR>
<BR>
Generating output...<BR>
<BR>
masking<BR>
<BR>
done<BR>
<BR>
formating database...<BR>
<BR>
#--------- command -------------#<BR>
<BR>
Widget::formater:<BR>
<BR>
/home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0<BR>
<BR>
#-------------------------------#<BR>
<BR>
running blast search.<BR>
<BR>
#--------- command -------------#<BR>
<BR>
Widget::blastx:<BR>
<BR>
/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<BR>
<BR>
#-------------------------------#<BR>
<BR>
FATAL: Argument 1 ("-db") is not recognized or is improperly formed.<BR>
<BR>
EXIT CODE 5<BR>
<BR>
FATAL: Argument 1 ("-db") is not recognized or is improperly formed.<BR>
<BR>
EXIT CODE 5<BR>
<BR>
ERROR: BLASTX failed<BR>
<BR>
ERROR: Failed while doing blastx repeats<BR>
<BR>
ERROR: Chunk failed at level:1, tier_type:1<BR>
<BR>
FAILED CONTIG:contig-dpp-500-500<BR>
<BR>
<BR>
<BR>
ERROR: Chunk failed at level:2, tier_type:0<BR>
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FAILED CONTIG:contig-dpp-500-500<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
--Next Contig--<BR>
<BR>
<BR>
<BR>
Processing run.log file...<BR>
<BR>
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<BR>
<BR>
did not finish on the last run and must be erased<BR>
<BR>
#---------------------------------------------------------------------<BR>
<BR>
Now retrying the contig!!<BR>
<BR>
SeqID: contig-dpp-500-500<BR>
<BR>
Length: 32156<BR>
<BR>
Tries: 2!!<BR>
<BR>
#---------------------------------------------------------------------<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
re reading repeat masker report.<BR>
<BR>
/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<BR>
<BR>
running blast search.<BR>
<BR>
#--------- command -------------#<BR>
<BR>
Widget::blastx:<BR>
<BR>
/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<BR>
<BR>
#-------------------------------#<BR>
<BR>
FATAL: Argument 1 ("-db") is not recognized or is improperly formed.<BR>
<BR>
EXIT CODE 5<BR>
<BR>
FATAL: Argument 1 ("-db") is not recognized or is improperly formed.<BR>
<BR>
EXIT CODE 5<BR>
<BR>
ERROR: BLASTX failed<BR>
<BR>
ERROR: Failed while doing blastx repeats<BR>
<BR>
ERROR: Chunk failed at level:1, tier_type:1<BR>
<BR>
FAILED CONTIG:contig-dpp-500-500<BR>
<BR>
<BR>
<BR>
ERROR: Chunk failed at level:2, tier_type:0<BR>
<BR>
FAILED CONTIG:contig-dpp-500-500<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
--Next Contig--<BR>
<BR>
<BR>
<BR>
Processing run.log file...<BR>
<BR>
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<BR>
<BR>
did not finish on the last run and must be erased<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
Maker is now finished!!!<BR>
<BR>
<BR>
<BR>
bioinf@linux-hdoc:~/Desktop/TEMP><BR>
<BR>
<BR>
<BR>
<BR>
Can you please help me?<BR>
Thanks<BR>
<BR>
Joana</FONT>
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