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Error: Unknown argument: "max_hsps_per_subject"

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Error: Unknown argument: "max_hsps_per_subject"

Quanwei Zhang
Hello:

I want to assign gene function to the predicted genes. I collected UniProt/SwissProt human, mouse and rat protein sequences (including both canonical and isoforms). Then use "makeblastdb" to build the database. And then run "blastp -db ... -max_hsps_per_subject 1" following the example in the protocol. But it returns me an error: Unknown argument: "max_hsps_per_subject".  Why this happens? Is it because I am using a different version of blastp?

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]
    [-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]
    [-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]
    [-line_length line_length] [-html] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
    [-use_sw_tback] [-version]

 Thanks
Best
Quanwei

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Re: Error: Unknown argument: "max_hsps_per_subject"

Michael Campbell
Hi Quanwei,

Different versions/implementations of blast do have parameters. Based on the usage you posted my guess is that the parameter you want is “-max_hsps”

Thanks,
Mike

> On Feb 10, 2017, at 11:53 PM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> I want to assign gene function to the predicted genes. I collected UniProt/SwissProt human, mouse and rat protein sequences (including both canonical and isoforms). Then use "makeblastdb" to build the database. And then run "blastp -db ... -max_hsps_per_subject 1" following the example in the protocol. But it returns me an error: Unknown argument: "max_hsps_per_subject".  Why this happens? Is it because I am using a different version of blastp?
>
> 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]
>     [-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]
>     [-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]
>     [-line_length line_length] [-html] [-max_target_seqs num_sequences]
>     [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
>     [-use_sw_tback] [-version]
>
>  Thanks
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Error: Unknown argument: "max_hsps_per_subject"

Quanwei Zhang
Thanks. Yes, I should use "-max_hsps".

Best
Quanwei

2017-02-13 9:02 GMT-05:00 Michael Campbell <[hidden email]>:
Hi Quanwei,

Different versions/implementations of blast do have parameters. Based on the usage you posted my guess is that the parameter you want is “-max_hsps”

Thanks,
Mike
> On Feb 10, 2017, at 11:53 PM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> I want to assign gene function to the predicted genes. I collected UniProt/SwissProt human, mouse and rat protein sequences (including both canonical and isoforms). Then use "makeblastdb" to build the database. And then run "blastp -db ... -max_hsps_per_subject 1" following the example in the protocol. But it returns me an error: Unknown argument: "max_hsps_per_subject".  Why this happens? Is it because I am using a different version of blastp?
>
> 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]
>     [-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]
>     [-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]
>     [-line_length line_length] [-html] [-max_target_seqs num_sequences]
>     [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
>     [-use_sw_tback] [-version]
>
>  Thanks
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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