[maker-devel] 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 <michael.s.campbell1 at gmail.com>:

> 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 <qwzhang0601 at gmail.com>
> 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
> > _______________________________________________
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> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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