BLAST, OID not found

Question

[tcf.hcdg]

Hello

I am running standalone BLAST version 2.2.31 locally on my computer. I wanted to do BLASTp against swissprot database. For this I downloaded the data base and configured the system according to the manual.

For single query it is working well but with batch option it is giving the error. "OID not found"

Can anybody tell me what is wrong with the commands. Here is my command which I am using

C:\myprog\blast-2.2.31+>blastdbcmd -db C:\myprog\blast-2.2.31+\db\swissprot\swissprot -entry_batch "CSAI_contig04661_1_6frame_translation.txt" -outfmt "%f" -out test_pro_bat_art.txt
Error: [blastdbcmd] >CSAI_contig04661_1: OID not found
Error: [blastdbcmd] EERNISFHSECVVNRQLKLAFDNSQVLKCCPETNNISGTDKPHLNQVGLYFVGTNGIFVI
APSFFPRTAILTLVPDLCDPDFTYPIAMFFFRQGLNPPLVTSPMFSPFSFLISLWPLAGGPEEIKPTRLIDGPVSSCLRI
TSAPRKPPSALLLFPIAHVSPASTGVMCCSISLPYKHSPASSLRLSRAPKPVSLTFPSDFSKIALARSTAFSEGTEISNP
SSPVYPVLVRKHFEPLISNTRKSPKYILLKSSFIKCRVGAARGPRAKRDLSSMCHETSPPLDLNTFMCSSMAKSLSLHPA
LTTKYISSVTLVITESSIAPPFSFVNTVRVPVPLASEATSAITSFSRKEMLSFPLRLSPHMCETSKRLPFSLQLTVESMI
ESLYIGMLHPANGTIFPPLATWKSRTVFLSSDSAEYLRATAFLSACARRRVIDWPSCHKPPLIFNTKSIDCGLCSTVSLA
FQKNANLRAQKTISHQERDWLLYICVCICLCKALKRDNVSKYVYCSRKKNNNNKK: OID not found
Error: [blastdbcmd] >CSAI_contig04661_2: OID not found
Error: [blastdbcmd] KKETFHSIQNVWIDNNHLTETVKFYENAVHEKRIRIFLELISHTIRLACSILVQMAFLPH
HSSFLELQSLWSLTCVIQISHIPLCSSSGKDILHSLPQCFHPSHSSHCGLLLGDLKRSNQHASMDLFPVVGSPQHPESHL
LPFFSSLPMLVQPQQVCVVPYHCHTNTVLLPVDYPEHPNPSVSPFLLTFPRLLWQDPLHSQKEQKFQIHLHLCTRFWGSI
LSHFPTLGSLQNISCSNHLSLSVEELEQQEGPEELKEISHHECAMRHLHLITLSCAPQCEPNPYPCIQHPPSIYDHQPWS
QSHQHHPSHLIQEFQFHWQARQHQQQVSQGKKCCLFPGSVHTCVRHQKDSRSPYNQSPLSLCTEACSTQQMAPSFHHQHG
NHKEQSFAQIPQNNIYELPPSYQPVQGGGLIGQVAINPLSFSIQKVSTVKDCAVLYPWLFRKMQIEPKRPYPTKKEIGFY
IYVCVYASARHREIMYPNMCTAVEKKIIIIKK: OID not found
Error: [blastdbcmd] >CSAI_contig04661_3: OID not found
Error: [blastdbcmd] RKKHFIPFRMCGKTIEISILKQSSFMKMLSMRNELEYFWNATPKSGWLVVFCRYKWHFCD
SPIIVLSSNCNLNFGPLVSRFHISHSYVLLQARTKSSTRDFPNVFTLLILNLTVASCWGTRDQTNTPDRWTCFQLFEDHL
STQKATFCPSSLPYSPCSSLNRCDVLFHIIAIQTQSCFQSKTIPSTQTRQSHLSFLFQDCFGKIHCILRRNRNFKSIFTC
VPGSGEEAFAIDFQHSEVSKIYLAQIIFHVLKSWSSKRALKSKRSLIMNVPDISTFRFEHFHVLLNVSQILIPASSIDHQ
VYMIISNLGDHRVINSTTLLICKYSKSSSSIGKRGNISNNKFLKERNAVFSLEAQSTHVDIKKTPVLPTIDSRVHDVFVL
NRHAPPSKWHHLSTISNMEIIKNSLFELRFRRIISTSYRLLISLCKAAGDLAKLPTPSHFQYKKYRLLRIVQYCILGFSE
KCKSESPKDHIPPRKRLAFIYMCVYMPLQGTEERCIQICVLQKKKK: OID not found
Error: [blastdbcmd] >CSAI_contig04661_4: OID not found
Error: [blastdbcmd] FFIIIIFFSTAVHIFGYIISLQCLAEAYTHTYIKPISFLVGYGLLGSQICIFLKSQGYST
AQSLTVDTFCIENERGFMATWPINHPPPCTGEGGSSILFCGIAQKDCSLFPCCWWKDGAICWVEHAYSVQRLNHGLYCQL
GERESFCLTHVWTEPQGKRQHFFPETCYCCCLACQWNWNSYCIYKEGWCYLCDHQGYSYILGGQCWMQGGFGSHGAHESV
QIRWRCLMAHSEISFSSSGPSCCSNSSTLNERFEQDIFWRLPSVGNQWLKMLPHQNRVHRRWINFCSFECSGSCQSNLGK
VRRKGETDGFGCSGSTGSRTVFVWQYGTTHHTCGWTNMGYREEKKGRRWLSGCGDPQTTGNRSIDQACWFDLFRSPSKRP
QDEEGKHWGSHEWRISLPEEEHSYGICEIWITQVRDQSDCSSRKELWGYHKNAICTYKILQANLIVWLISSRNILIRFSW
TAFSNLTVSVKCFQLSIYHTFMENVSFF: OID not found
Error: [blastdbcmd] >CSAI_contig04661_5: OID not found
Error: [blastdbcmd] FFYYYYFFFYCSTHIWIHYLSSVPCRGIYTHIYIKANLFLGGIWSFGLSDLHFSEKPRIQ
YCTILNSRYFLYKEGVYGNLANQSPAALHRLIRRRLVDIILRNLSSKRLFFMISMLLMVERWCHLLGGACLFSTKTQSWT
LLSIVGRTGVFLMSHTCVDASREKTAFLSLRNLLLLMLPRLPMELELLLYLQMRRVVLLMTLSPRLLMIIYTWWSMLDAG
IRIWLTLRSTKCSNLKVEMSHGTFMMRDLFLFRALLLLQLFNTKMIARYILETSECWKSMAQNASSPEPGTQVKMDLKFL
FLLRMQWILPKQSWKSQKERDRVWVLGIVLDWKQDCVCMAMIWNNTSHLLRLDHGLGREEGQKVAFWVLRSSNNWKQVHR
SGVLVSLQVPQQEATVRLRMRRVKTLGKSRVEDLVLARRTLWDMNLDHTSQGPKLRLQFEERTMMGLSQKCHLYLQNTTS
QPDLGVAYQFQKYSNSFLMDSIFIKLDCFSQMLISIVYLPHILNGMKCFFL: OID not found
Error: [blastdbcmd] >CSAI_contig04661_6: OID not found
Error: [blastdbcmd] FLLLLFFFLLQYTYLDTLSLFSALQRHIHTHIYKSQSLSWWDMVFWALRFAFFKAKDTVL
HNPQSILFVLKMRGGLWQLGQSITRRLAQADKKAVARRYYSAESELKKTVLYDFHVANGGKMVPFAGWSMPIQYKDSIMD
STVNCRENGSLFDVSHMCGLSLKGKDSISFLEKLVIADVASLANGTGTLTVFTNEKGGAIDDSVITKVTDDHIYLVVNAG
CRDKDLAHIEEHMKVFKSKGGDVSWHIHDERSLLALQGPLAAPTLQHLMKDDLSKIYFGDFRVLEINGSKCFLTRTGYTG
EDGFEISVPSENAVDLAKAILEKSEGKVRLTGLGARDSLRLEAGLCLYGNDMEQHITPVEAGLTWAIGKRRRAEGGFLGA
EVILKQLETGPSIRRVGLISSGPPARGHSEIKNEKGENIGEVTSGGFSPCLKKNIAMGYVKSGSHKSGTKVKIAVRGKNY
DGAITKMPFVPTKYYKPTFRCGLSVPEIFFVSHGQHFHKTLFQSNANFNCLFTTHSEWNEMFLSS: OID not found

Answer 1

[GenoMax]

If you are trying to do blastp search then "blastdbcmd" is not the right program. You want to use blastp.

Type blastp -help to see command line help. Command line options are here: http://www.ncbi.nlm.nih.gov/books/NBK279675/

An example command for your job would be something like this.

C:\myprog\blast-2.2.31+>blastp -db C:\myprog\blast-2.2.31+\db\swissprot\swissprot -query CSAI_contig04661_1_6frame_translation.txt -outfmt '0' -out
 test_pro_bat_art.txt

There are multiple command line options that will modify the output. Option '0' will give you pair-wise alignments. 7 would be tabular etc.

[tcf.hcdg]

Thanks. It works