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  • capricy
    Senior Member
    • Apr 2012
    • 125

    blastp error: Too many positional arguments (1), the offending value: std

    Hello, there,

    What I was trying to get is the format 6 standard output plus qlen. So, I am using the following command line:

    /projects01/tools/ncbi-blast-2.2.28+/bin/blastp -outfmt "6 std qlen" -matrix PAM30 -ungapped -comp_based_stats F -window_size 0 -xdrop_ungap 1 -evalue 1e-3 -max_target_seqs 1000000 -num_threads 8 -dbsize 27,736,644,057 -query /projects01/tools/VFG016041.faa -db /projects01/tools/biobakery-shortbred-01a17dc2f942/db-inHouse/mpiblast/refdb/uniref100/uniref100.fasta -out /projects01/tools/scr/test/blast-28-P-1-results

    but got the error message:

    USAGE
    blastp [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-max_hsps_per_subject int_value] [-seg SEG_options]
    [-soft_masking soft_masking] [-matrix matrix_name]
    [-threshold float_value] [-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] [-html]
    [-max_target_seqs num_sequences] [-num_threads int_value] [-ungapped]
    [-remote] [-comp_based_stats compo] [-use_sw_tback] [-version]

    DESCRIPTION
    Protein-Protein BLAST 2.2.28+

    Use '-help' to print detailed descriptions of command line arguments
    ========================================================================

    Error: Too many positional arguments (1), the offending value: std

    Could anyone help me to correct it?

    Thanks a lot!

    C.

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