Command Line BLAST Question

Question

[Randal]

I am utilizing this youtube video: to learn how to use command line BLAST to align my sequences. I am trying to use "blastp" rather than the "blastn" example in the video. I am using my own protein sequences because the files she mentioned in the video are no longer available. The issue is when I try to BLAST my sequences as she did in the video it states "Error: Too many positional arguments (1), the offending value:" What are you guys tips on creating a successful outcome as she did in the video.

Thank you in advance

[5heikki]

Please include the actual command that you used so that we can point out the mistake..

[Randal]

Here is the command:

randalburks@Randals-MacBook-Air ~ % blastp
BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified
Please refer to the BLAST+ user manual.
randalburks@Randals-MacBook-Air ~ % cd Desktop/Chicken/
randalburks@Randals-MacBook-Air Chicken % ls -F
ARG_06_01.fasta     HK_gene_06_01.fasta
randalburks@Randals-MacBook-Air Chicken % head ARG_06_01.fasta
>gi|34101385|gb|AAQ57754.1| DNA topoisomerase IV subunit A [Chromobacterium violaceum ATCC 12472]
MSDHDLFDSPAPAGDLTPPPPAAPEAASGDWIPLDLYAERAYLEYAMSVVKGRALPEVADGQKPVQRRIL
YAMRDMGLVHGAKPVKSARVVGEILGKYHPHGDSSAYEALVRMAQDFTLRYPLIDGQGNFGSRDGDGAAA
MRYTEARLTPIAELLLSEIDMGTVDFVPNYDGAFEEPSLLPARLPMVLLNGASGIAVGLATEIPPHNLTE
VAAACVALLDDPELDTAALMQYVPGPDFPGGGQIITPVADILSAYETGKGSVRVRAKWEVEKLARGQWRA
IVTELPPGSSAQKVLAEIEEATNPKLKAGKKQLSQDQQNLKKLMLDLLDRVRDESDSESPVRLVFEPKSS
RQDPDEFMNILLAQTSLEGNASLNLVMIGLDGRPGQKGLKPILTEWIDFRRTTVTRRLAHRLAQVDKRIH
ILEGRMIAFIHIDEVIRVIRESDEPKPDLIKAFGLTEIQAEDILEIRLRQLARLEGFKLEKELSELREER
EGLRHVLDTPDALTRLIRDEIQADAAKYGDKRRTEIKAAERAVLTQTTADEPVTLILSQKGWIRARVGHN
VELETLSFKDGDGLAAVVETRTVWNAIVLDHNGRAYTIDPATVPTGRGDGVPVASLVDLQDGAKPAQLIS
randalburks@Randals-MacBook-Air Chicken % tail ARG_06_01.fasta
ITLIPTPPVRGEIVDVNGVPLAKNYPVFSLEVIPSRIEGKMEDVIEALRKYVDITPTDLKRFHKYRESYR
KFENIPLKLRLTDEEAAKLSVHLNEFKGVEVNSRTFREYPYGKLTSHFLGYIGRISDKDQEILEEEGLTA
LYRGSTHIGKSGLEKFYEPQLHGAPGYQEVEKDAYGNIVRVLKNVPSRMGQTLRLGMDIRMQQEADKILG
DRRGAIVAINPQDGTVLAFVSKPSFDPNLFIDGIDSETWKALNDDWKKPLVNRVTQGLYPPGSTFKPFMG
MALLESGKITQTTVVPAPGAWSIPGSRHVFRDSVRSGHGSANLSKAIQVSSDTFFYRLGYEMGIDKASPY
LAQFGFGKKTGIDLPSEYTGVLPSREWKAKRFAKSSDPTAKEWRAGEMVSVSIGQGYNAYTPLQMAHATA
SLANNGVVYQPHLVKELLDFDKRKITRINPNPEYKIPFKQDNFEYVKQAMEKVLKPGGTAHRIGGGLAYS
MGGKTGTAQVVQIKQGGRYNAAALREQHRDHAWFISFAPLEKPEIAIAVILENGGWGAYAAPLARSLTDF
YMLNVKPQQFSDDPDAGGMPEPQQHRTQPQPPTIFQKAYGLKQEEANHE

randalburks@Randals-MacBook-Air Chicken % awk 'NR==1, NR==20' ARG_06_01.fastsa
awk: can't open file ARG_06_01.fastsa
 source line number 1
randalburks@Randals-MacBook-Air Chicken % awk 'NR==1, NR==20' ARG_06_01.fasta 
>gi|34101385|gb|AAQ57754.1| DNA topoisomerase IV subunit A [Chromobacterium violaceum ATCC 12472]
MSDHDLFDSPAPAGDLTPPPPAAPEAASGDWIPLDLYAERAYLEYAMSVVKGRALPEVADGQKPVQRRIL
YAMRDMGLVHGAKPVKSARVVGEILGKYHPHGDSSAYEALVRMAQDFTLRYPLIDGQGNFGSRDGDGAAA
MRYTEARLTPIAELLLSEIDMGTVDFVPNYDGAFEEPSLLPARLPMVLLNGASGIAVGLATEIPPHNLTE
VAAACVALLDDPELDTAALMQYVPGPDFPGGGQIITPVADILSAYETGKGSVRVRAKWEVEKLARGQWRA
IVTELPPGSSAQKVLAEIEEATNPKLKAGKKQLSQDQQNLKKLMLDLLDRVRDESDSESPVRLVFEPKSS
RQDPDEFMNILLAQTSLEGNASLNLVMIGLDGRPGQKGLKPILTEWIDFRRTTVTRRLAHRLAQVDKRIH
ILEGRMIAFIHIDEVIRVIRESDEPKPDLIKAFGLTEIQAEDILEIRLRQLARLEGFKLEKELSELREER
EGLRHVLDTPDALTRLIRDEIQADAAKYGDKRRTEIKAAERAVLTQTTADEPVTLILSQKGWIRARVGHN
VELETLSFKDGDGLAAVVETRTVWNAIVLDHNGRAYTIDPATVPTGRGDGVPVASLVDLQDGAKPAQLIS
GRDEDRFVVAGSGGYGFIAKIGDMAGRVKAGKAFITLDASETVLEPVKLPAAPLEQLQLVAASDSDRLLA
FPAAELKELAKGRGLMLMALDDGAALTAIGLVAGGKALLSTTSVRGKEAEEKLALEEFAGKRAKKGKLMP
KKWRVSRIRELPM

>gi|34103609|gb|AAQ59970.1| DNA gyrase, subunit A [Chromobacterium violaceum ATCC 12472]
MTDNLFAKETLPISLEEEMRRSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMHELSNDWNRAYKKSAR
IVGDVIGKYHPHGDTAVYDTIVRLAQDFSLRYPLVDGQGNFGSVDGDNAAAMRYTEIRMARIAHELLADI
EKETVDFGPNYDGSEHEPLILPAKIPNLLVNGSSGIAVGMATNIPPHNLNEVVDACLALLANSDLTIDEL
IDIIPAPDFPTAGIIYGTAGVKEGYRTGRGRVIMRARTHTEPIGKGDREAIIVDEIPYQVNKARLLERIS
ELVRDKQIEGISDLRDESDKSGMRVVIELKRGEMPEVVLNHLFKMTQLQDSFGMNMVALVDGQPRLLNLK
randalburks@Randals-MacBook-Air Chicken % awk 'NR==1, NR==20' ARG_06_01.fasta > my_seqs_f
randalburks@Randals-MacBook-Air Chicken % ls -F
ARG_06_01.fasta     HK_gene_06_01.fasta my_seqs_f
randalburks@Randals-MacBook-Air Chicken % blastp -query my_seqs_f -db Chromobacterium violaceum ATCC 12472 -out my_seqs_blast.txt 
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 2.11.0+

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

Error: Too many positional arguments (1), the offending value: violaceum
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: violaceum
randalburks@Randals-MacBook-Air Chicken % 

[5heikki]

blastp -query my_seqs_f -db Chromobacterium violaceum ATCC 12472 -out my_seqs_blast.txt

-db should be followed by a valid database name. You can see from the error report that your problem lies here: the offending value: violaceum

Also we can see that you don't have a database with that name at least in the dir you are in. Have you setup a blastdb dir and is blast aware of it? I have a feeling that you haven't. Anyway if you have and that is a valid database name, then wrap it in single quotes:

-db 'Chromobacterium violaceum ATCC 12472'

Generally speaking there's little to be gained by creating a blast database consisting of just one bacterial genome. Instead of -db you would use -subject whateverFile.fasta

[Randal]

Thank you for your input I will definitely take that into account. My other question is , what should the database file consist of?

[5heikki]

You make blast databases from fasta files with the makeblastdb tool..