blastp 2.10.1+ custom outfmt error

Question

[Yanpeng Chen]

blastp -query protein.faa -db protein -outfmt "6 std qlen slen" -out protein.blastpcustom -evalue 10e-6

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] [-negative_seqidlist filename] [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename] [-negative_taxidlist filename] [-ipglist filename] [-negative_ipglist 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] [-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] [-subject_besthit] [-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] [-sorthits sort_hits] [-sorthsps sort_hsps] [-max_target_seqs num_sequences] [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION Protein-Protein BLAST 2.10.1+

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

========================================================================

Error: Too many positional arguments (1), the offending value: std Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: std enter image description here

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Hi guys,

I just know what caused the error. I download the precomplied executables, it was not compatible with my HPC system, although most of them can be invoked successfully. Today, I installed the 2.10.1 using conda install -c bioconda blast=2.10.1, the error didn't happen.

If you want add additional infor besides std, you can use the expression -outfmt "7 std qlen slen" in blast v2.10.1. Result format is as follows.

I help this post can help other people who have the same problem.

# BLASTX 2.10.1+
# Query: NC_030954.1
# Database: 5000prot
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, query length, subject length
# 1927 hits found
NC_030954.1     sp__C9SM62__VPS10_VERA1 68.791  1522    379     12      3134808 3139358 1       1431    0.0     2121    6042495 1447
NC_030954.1     sp__Q4PFV5__DPOE_USTMA  47.849  2069    935     32      4748540 4754470 285     2301    0.0     1803    6042495 2305
NC_030954.1     sp__Q4PFV5__DPOE_USTMA  42.553  235     131     2       4747765 4748469 53      283     2.56e-43        183     6042495 2305
NC_030954.1     sp__Q6C4J0__DPOE_YARLI  42.921  2027    1023    33      4748540 4754449 224     2173    0.0     1556    6042495 2183
NC_030954.1     sp__Q6C4J0__DPOE_YARLI  28.054  221     120     3       4747810 4748472 42      223     8.06e-18        99.0    6042495 2183
NC_030954.1     sp__Q10178__SF3B1_SCHPO 61.859  1151    373     13      1447631 1444224 102     1201    0.0     1407    6042495 1205
NC_030954.1     sp__A7ERM5__ATG26_SCLS1 59.224  1263    388     21      5867635 5871321 228     1397    0.0     1350    6042495 1435
NC_030954.1     sp__A7ERM5__ATG26_SCLS1 34.896  192     105     5       548811  549386  935     1106    1.68e-49        119     6042495 1435
NC_030954.1     sp__A7ERM5__ATG26_SCLS1 39.695  131     65      4       549684

Answer 1

[Mensur Dlakic]

There is no need to past the whole BLAST command line summary. The last line with the error is enough, and it tells you that the offending value is std inside the quotation marks of your outfmt. Here are allowed options:

http://www.metagenomics.wiki/tools/blast/blastn-output-format-6

This post may be useful as well.

[Yanpeng Chen]

I appreciate your reply. The BLAST command line posted above worked well in version 2.5.0+.And if we do not specify the tag 'std', the result will contains only 2 columns data: qlen slen. I think the point of the problem is related to BLAST version 2.10.1+, maybe this new version require different format to custom outfmt. I hope anyone else who encounttered same error to share the experience and resolutions.

[Mensur Dlakic]

The old std does not exist in this version. If you typed blastp -help, you would see that it is equivalent to:

-outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore"

So you may want to try -outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen" and see if that is you what you need.

[Yanpeng Chen]

$blastp -query protein.faa -subject protein.faa -out  protein_s_j_customed.blastp -outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen" -evalue 10e-6

Same error

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

Error: Too many positional arguments (1), the offending value: qaccver
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: qaccver

[Mensur Dlakic]

With all due respect, how is it the same error? It clearly says the offending value: qaccver which is different. It also tells you that by typing -help you will get detailed descriptions, and I suggest you do that and figure out how you want the output format to look like.

[Yanpeng Chen]

Thanks for your reply. I got the cause today and update this post