mattb112885
commented
8 years ago Sorry, You don't have the latest version. Your help should look like this if you have a recent enough version (after 2.2.28). It may not be the latest in your package manager -- you can download it from here:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
USAGE rpsblast [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-db database_name] [-dbsize num_letters] [-entrez_query entrez_query] [-query input_file] [-out output_file] [-evalue evalue] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-lcase_masking] [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-comp_based_stats compo] [-use_sw_tback] [-version]
DESCRIPTION Reverse Position Specific BLAST 2.3.0+
Use '-help' to print detailed descriptions of command line arguments
Everything is updated regarding blast+ and rpsblast on my machine, but rpsblast has different arguments now and so instead of -query it uses -i and -d for database instead of -db and -o for output instead of -o etc. This needs to be updated within the setup_step4.sh because currently it does not function due to the invalid arguments.
Example: rpsblast -query faa/6666666.173663.txt.faa -db cd_db/Cdd.pn -out rpsblast_res/6666666.173663.txt.faa_rpsout -outfmt 6 -evalue 1.000000e-05 [rpsblast] ERROR: Invalid argument: -query
I can do it by hand and it works: rpsblast -i faa/6666666.168144.txt.faa -d cd_db/Cdd.pn -o rpsblast_res/6666666.168144.txt.faa_rpsout -e 1e-05 -m 1 -a 16
Thanks.