PHMMER on XSEDE 3.3.2 Biological sequence analysis using profile hidden Markov models - run on XSEDE Sean Eddy http://www.hmmer.org Sequence Analysis phmmer_xsede phmmer_comet perl "phmmerwrapper_3.3.2_comet" 0 number_nodes 2 scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=$num_cores\\n" mpi_run 2 scheduler.conf perl $run_mpi perl "run_type=mpi\\n" infile_seq Input File (the query sequence file) perl "seqfile.txt" 98 seqfile.txt all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours for non-gpu; 120 for gpu jobs) 0.5 The maximum runtime for a job can be no more than 168 hours perl $runtime > 168.0 perl "runhours=$value\\n" The job will run on $num_cores processors as configured. If it runs for the entire configured time, it will consume $num_cores X $runtime cpu hours perl $runtime > 0 && defined $num_cores The job will run on $num_cores processors as configured. If it runs for the entire configured time, it will consume $num_cores X $runtime cpu hours perl $runtime > 0 && $run_mpi Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less dependably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. num_cores How many cores do you need? perl "--cpu $value" 2 20 Please enter an integer for the number of cores. perl !defined $num_cores Sorry you cant use mpi and cpu commands perl defined $num_cores && $run_mpi This option will help the application determine how to run the job seed_val Enter the seed value here perl $spec_seed perl "--seed $value" 42 20 select_database Enter the database file here user_dataset.txt perl "user_dataset.txt" 99 scoring_options Options Controlling Scoring System set_gapvalue Gap open probability for a single sequence query model (--popen) perl defined $value ? "--popen $value":"" 0.02 Please choose a gap probability value greater than 0 and less than 0.5 perl $set_gapvalue <= 0 || $set_gapvalue > 0.5 25 set_gapextendvalue Gap extend probability for a single sequence query model (--pextend) perl defined $value ? "--pextend $value":"" 0.4 25 Please choose a gap probability value greater than 0 and less than 0.5 perl $set_gapextendvalue < 0 || $set_gapextendvalue >= 1.0 specify_alignprobs Obtain residue alignment probabilities from this substitution matrix (--mx) PAM30 PAM70 PAM120 PAM240 BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 perl $value ? "--mx $value":"" 25 custom_mxfile Obtain residue alignment probabilities from custom substitution matrix (--mxfile) perl defined $dombitscore ? "--mxfile custom_submatrix.txt":"" custom_submatrix.txt 25 reporting_options Options Controlling Reporting Thresholds set_evalue Report target sequences with an E-value of (-E) perl defined $value ? "-E $value":"" 10.0 5 specify_bitscore Report target sequences with a bit score of (-T) perl defined $specify_bitscore ? "-T $specify_bitscore":"" 10 Sorry you cant specify both -T and -domE perl defined $specify_bitscore && defined $set_evalue specify_domevalue Conditional E-value for individual domains (--domE) perl $value ? "--domE $value":"" 10.0 8 specify_dombitscore Report domains with bit score value of (--domT) perl defined $dombitscore ? "--domT $value":"" 10 Sorry you cant specify both -domT and -domE perl defined $specify_dombitscore && defined $set_domevalue output_options Options Controlling Output output_file Write output to this file (-o) perl defined $value ? "-o $output_file":"" 40 multialignment_file Save a multiple alignment of all significant hits (-A) perl defined $value ? "-A $multialignment_file":"" 40 tblout_file Save simple tabular file summarizing per-target output (-tblout) perl defined $value ? "--tblout $tblout_file":"" 2 domtblout_file Save a simple tabular file summarizing the per-domain output (-domtblout) perl defined $value ? "--domtblout $domtblout_file":"" 3 pfamtblout_file Save tabular file summarizing the per-target output (-pfamtblout) perl defined $value ? "--pfamtblout $pfamtblout_file":"" 4 use_accessions Use accessions instead of names in the main output (--acc) perl $value ? "--acc":"" 10 omit_alignment Omit the alignment section from the main output. (--noali) perl $value ? "--noali":"" 10 unlimit_length Unlimit the length of each line in the main output (--notextw) perl $value ? "--notextw":"" 10 setlimit_length Limit the main output’s line length (--textw) perl defined $unlimit_length ? "--textw $value":"" 10 h3parameter_estimation Options Controlling H3 Parameter Estimation specify_seqlength Specify the sequence length in simulation (--EmL) perl defined $specify_seqlength ? "--EmL $value":"" 200 15 specify_seqnum Sets the number of sequences to estimate mu for MSV (--EmN) perl defined $specify_seqlength ? "--EmN $value":"" 200 15 specify_seqlength2 Length of sequence to estimate mu for Viterbi (--EvL) perl defined $specify_seqlength2 ? "--EvL $value":"" 200 15 specify_seqnum2 Number of sequences to estimate mu for Viterbi (--EvN) perl defined $specify_seqnum2 ? "--EvN $value":"" 200 15 specify_seqlength3 Sequence length to estimate tau (--EfL) perl defined $specify_seqlength3 ? "--EfL $value":"" 100 15 specify_seqnum3 Sequence number to estimate tau (--EfN) perl defined $specify_seqnum3 ? "--EfN $value":"" 200 15 specify_tailmassfr Sets the tail mass fraction (--Eft) perl defined $specify_seqnum3 ? "--Eft $value":"" 0.04 15 pipeline_options Options Controlling the Acceleration Pipeline disable_filters Turn off all filters (--max) perl $value ? "--max":"" 0 27 specify_pvalue Set the P-value threshold for the MSV filter step (--F1) perl defined $specify_pvalue ? "--F1 $value":"" 0.02 10 specify_pvalue2 Set the P-value threshold for the Viterbi filter step (--F2) perl $specify_pvalue2 ? "--F2 $specify_pvalue2":"" 0.001 10 specify_pvalue3 Set the P-value threshold for the Forward filter step (--F3) perl defined $specify_pvalue3 ? "--F3 $specify_pvalue3":"" 0.00001 10