wyim-pgl/dcblast

Divide and Conquer BLAST: using grid engines to accelerate NCBI-BLAST+ and other sequence analysis tools

dcblast's Issues

Support for Torque/PBS

Hi,
I would like to use dcblast to submit jobs to PBSpro. It could use a template file and replace the variables. For my purposes the following template would be enough.

#PBS -S $my_shell
#PBS -q $queue_name
#PBS -N ${job_prefix}_${chunk_id}
#PBS -l select=1:ncpus=24,walltime=144:00:00
#PBS -A $project_name
#PBS -M $email
#PBS -m ea

cd $PBS_O_WORKDIR || exit 255

$blastcmd" "${args}" "${other_user_opts}"

The command to submit a job is:

qsub "${pbs_script_filename}"

Reg:No output from the run

hi,
After i execute the command ,the job goes to failed state,without any error or log...

Please help.

Implementation to other HPC systems

Dear @Ascendo,
I read your paper and find your tool fascinating. Any plans of implementing a version of this for LSF? If not, do you have any suggestion on how I may go about speeding up blastn on an LSF cluster?

slurm script error: dcblast_merge.sh: command not found

I tried it and got an error
dcblast_split.sh: command not found
dcblast_merge.sh: command not found

I solved this issue by editing the line 56 and 57 from:
my $dcblast_blastcmd = 'dcblast_blastcmd.sh';
my $dcblast_mergecmd = 'dcblast_merge.sh';

To:
my $dcblast_blastcmd = './dcblast_blastcmd.sh';
my $dcblast_mergecmd = './dcblast_merge.sh';

The system now can find the two scripts.

Jobs stuck in Eqw or hqw states

Hi Dear Won Chol,

Thank you for developing DCBLAST.

Currently, we are trying to use DCBLAST to perform blastp on our Sun Grid Engine System.

The command we were using is:
perl dcblast.pl --ini configL.ini --input L6_Fv.faa --size 200 --output L6_Fv_vs_nr2 --blast blastp

We noticed that the .faa file was split successfully. However, the jobs were in Eqw or hqw states. Upon checking the error underlying Eqw state, we noticed that it is related to password entry error for the user ('can't get password entry for user "xxx". Either the user does not exist or NIS error!'); the user account is available on head node but not on the compute node.

Hope you may be able to advise on how we can resolve the problem.

Thanks.

PBS code hack?

PBS & LSF need simple code hack. If you need it please request through issue.

I am running dcblast.pl through PBS and only the first result file gets written-no other results files are created. Pls help.

See my config below:
`[dcblast]
##Name of job (will use for SGE job submission name)
job_name_prefix=dcblast_benchmark

[blast]
##BLAST options

##BLAST path (your blast+ path)
path=/data-fastpool/ncbi-blast-2.10.0+/bin

##DB path (build your own BLAST DB)
##example
##makeblastdb -in example/test_db.fas -dbtype nucl (for nucleotide sequence)
##makeblastdb -in example/your-protein-db.fas -dbtype prot (for protein sequence)
db=/data-fastpool/FELIX/blastdb/AllProteins/upkb_reviewed/upkb_bact_swissprot.fasta

##Evalue cut-off (See BLAST manual)
evalue=1e-05

##number of threads in each job. If your CPU is AMD it needs to be set 1.
num_threads=12

##Max target sequence output (See BLAST manual)
max_target_seqs=1

##Output format (See BLAST manual)
outfmt=6

##any other option can be add it this area
#num_alignments=1
#seg=yes
#soft_masking=true
#lcase_masking=
#max_hsps=1
#matrix=BLOSUM62
#gapopen=11
#gapextend=1

[sge]
##Grid job submission commands
##please check your job submission scripts
##Especially Queue name (q) and Threads option (pe) will be different depends on your system
M=[email protected]
d=/data-fastpool/FELIX/blastdb/AllProteins/upkb_reviewed
o=/data-fastpool/FELIX/working/swist/dcblast_test
e=/data-fastpool/FELIX/working/swist/dcblast_test
l=walltime=48:00:00,nodes=1:ppn=12,pmem=6gb
m=abe`