blastx: Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
Closed this issue · 1 comments
chamalis commented
:$ /usr/bin/time -v ./gawn 02_infos/gawn_config.sh
----------------------------------------------
GAWN v0.3 - Genome Annotation Without Nightmares
----------------------------------------------
02_infos/gawn_config.sh
GAWN: Skipping genome indexing
_______________________________________________________________________
/ \
| GAWN: Annotating genome with transcriptome
| --------------------------------------------------------------------- |
| |
\_______________________________________________________________________/
_______________________________________________________________________
/ \
| GAWN: Annotating transcriptome with swissprot
| --------------------------------------------------------------------- |
Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
To silence this citation notice: run 'parallel --citation'.
parallel: Warning: A record was longer than 1000. Increasing to --blocksize 1301.
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
USAGE
blastx [-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] [-negative_seqidlist 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] [-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] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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
Translated Query-Protein Subject BLAST 2.7.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Too many positional arguments (1), the offending value: -
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -
Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
To silence this citation notice: run 'parallel --citation'.
| |
\_______________________________________________________________________/
_______________________________________________________________________
/ \
| GAWN: Annotating genome using transcriptome
| --------------------------------------------------------------------- |
| |
\_______________________________________________________________________/
Command being timed: "./gawn 02_infos/gawn_config.sh"
User time (seconds): 0.42
System time (seconds): 0.18
Percent of CPU this job got: 103%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.58
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 28816
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 4
Minor (reclaiming a frame) page faults: 43291
Voluntary context switches: 466
Involuntary context switches: 111
Swaps: 0
File system inputs: 168
File system outputs: 9192
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
chamalis commented
False alarm. I had renamed SWISSPROT_DB in gawn_config.sh and forgot to revert it to the git state.