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.
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.