[EMBOSS] Impossible t ofetch a sequence from srs internet site with "seqret" command

simon stockes simonstockes at yahoo.fr
Sat Nov 29 14:29:12 UTC 2003


Hi All,

I'm trying to fetch a sequence from srs site with "seqret" command and 
got an error. This error was obtain from
"seqret -debug qasrswww:HSCAD5 HSCAD5.fasta" commande line and the 
emboss.default part corresponding is :

DB qasrswww [
	type: "N"
	format: "embl"
	methodquery: "srswww"
	dbalias: "EMBL"
	fields: "sv des org key"
	url: "http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz"
	comment: "Remote SRS web server"
]

Config Mac OS 10.2.8, G3 ibook, /usr/local installation (with fink 
installation I got the same error).
I suspect there is no proxy between me and the srs server.
The seqret.dbg file (see below) says : it get the sequence file but 
there is a problem after ....


Hope tracks,

Simon.

seqret.dbg
=========

Debug file seqret.dbg buffered:No
ajFileNewIn '/usr/local/emboss/share/EMBOSS/acd/seqret.acd'
EOF ajFileGetsL file /usr/local/emboss/share/EMBOSS/acd/seqret.acd
closing file '/usr/local/emboss/share/EMBOSS/acd/seqret.acd'
ajFeatTabInNew 1b1320
ajSeqinClear called
ajFeattabInClear called
++seqUsaProcess 'qasrswww:HSCAD5' 0..0(N) '' 0
USA to test: 'qasrswww:HSCAD5'

format regexp: No list:No
no format specified in USA

...input format not set
dbname dbexp: Yes
found dbname 'qasrswww' level: '<null>' qry->QryString: 'HSCAD5'
seqQueryFieldC usa 'sv' fields 'sv des org key'
seqQueryField test 'sv'
seqQueryField match 'sv'
ajSeqQueryWild id 'HSCAD5' acc 'HSCAD5' sv 'HSCAD5' des '' org '' key ''
wild (has) query Sv 'HSCAD5'
database type: 'N' format 'embl'
use access method 'srswww'
Matched seqAccess[3] 'srswww'
seqAccessSrswww EMBL:HSCAD5
seqHttpUrl http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz
searching with SRS url 'GET 
/srs71bin/cgi-bin/wgetz?-e+-ascii+[EMBL-id:HSCAD5]|[EMBL-acc:HSCAD5]'
httpver getValueC '<null>'
httpver after qry '<null>'
host 'www.infobiogen.fr' port 80 get 'GET 
/srs71bin/cgi-bin/wgetz?-e+-ascii+[EMBL-id:HSCAD5]|[EMBL-acc:HSCAD5] 
HTTP/1.0
'
gethostbyname host 'www.infobiogen.fr' returns 'babbage.infobiogen.fr' 
errno 0 hp_addr 193.52.226.5
creating socket
setup socket data
connecting to socket 4
sin sizeof 16
connect status 0 errno 0 msg 'Successful system call (0 - Undefined 
error: 0)'
inet_ntoa '193.52.226.5'
sending: 'GET 
/srs71bin/cgi-bin/wgetz?-e+-ascii+[EMBL-id:HSCAD5]|[EMBL-acc:HSCAD5] 
HTTP/1.0
' status: 82
send for GET errno 0 msg 'Successful system call (0 - Undefined error: 
0)'
sending: 'Host: www.infobiogen.fr:80
' status: 27
send for host errno 0 msg 'Successful system call (0 - Undefined error: 
0)'
sending: '
' status: 1
send for blankline errno 0 msg 'Successful system call (0 - Undefined 
error: 0)'
fdopen errno 0 msg 'Successful system call (0 - Undefined error: 0)'
EOF ajFileGetsL file
End of file - data in buffer - return ajFalse
First line [1] 'HTTP/1.1 200 OK
'
fileBuffLineDel removing line [1], 'HTTP/1.1 200 OK
' len 16
first line gone, new start [1] 1b5e60, '
' len 1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
first line gone, new start [1] 1b5dd0, 'Date: Sat, 29 Nov 2003 09:46:49 
GMT
' len 36
:[1] Date: Sat, 29 Nov 2003 09:46:49 GMT
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line  [1] 1b5ea0, 'Server: Apache/1.3.27 (Unix) mod_perl/1.27 
PHP/4.3.1
' len 53
:[1] Server: Apache/1.3.27 (Unix) mod_perl/1.27 PHP/4.3.1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line  [1] 1b6010, 'Connection: close
' len 18
:[1] Connection: close
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line  [1] 1b60a0, 'Content-Type: text/plain
' len 25
:[1] Content-Type: text/plain
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line  [1] 1b6130, '
' len 1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line  [1] 1b6170, '
' len 1
<blank line deleted> [1]
fileBuffLineDel removing line [1], '
' len 1
new next line  [1] 1b61b0, 'ID   HSCAD5     standard; mRNA; HUM; 3170 
BP.
' len 46
:[1] ID   HSCAD5     standard; mRNA; HUM; 3170 BP.
:[1] XX
:[1] AC   X59796;
:[1] XX
:[1] SV   X59796.1
:[1] XX
:[1] DT   12-FEB-1992 (Rel. 30, Created)
:[1] DT   24-JAN-1995 (Rel. 42, Last updated, Version 6)
:[1] XX
:[1] DE   H.sapiens mRNA for cadherin-5
:[1] XX
:[1] KW   cadherin.
:[1] XX
:[1] OS   Homo sapiens (human)
:[1] OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 
Euteleostomi; Mammalia;
:[1] OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
:[1] XX
:[1] RN   [1]
:[1] RP   1-3169
:[1] RA   Suzuki S.;
:[1] RT   ;
:[1] RL   Submitted (16-MAY-1991) to the EMBL/GenBank/DDBJ databases.
:[1] RL   S. Suzuki, Doheny Eye Institute, 1355 San Pablo St, Los 
Angeles, CA 90033,
:[1] RL   USA
:[1] XX
:[1] RN   [2]
:[1] RP   1-3169
:[1] RX   MEDLINE; 91283540.
:[1] RX   PUBMED; 2059658.
:[1] RA   Suzuki S., Sano K., Tanihara H.;
:[1] RT   "Diversity of the cadherin family: evidence for eight new 
cadherins in
:[1] RT   nervous tissue";
:[1] RL   Cell Regul. 2(4):261-270(1991).
:[1] XX
:[1] RN   [3]
:[1] RP   1-3170
:[1] RA   Suzuki S.;
:[1] RT   ;
:[1] RL   Submitted (24-JAN-1995) to the EMBL/GenBank/DDBJ databases.
:[1] RL   S. Suzuki, Doheny Eye Institute, 1355 San Pablo St, Los 
Angeles, CA 90033,
:[1] RL   USA
:[1] XX
:[1] DR   GOA; P33151.
:[1] DR   SWISS-PROT; P33151; CAD5_HUMAN.
:[1] XX
:[1] FH   Key             Location/Qualifiers
:[1] FH
:[1] FT   source          1..3170
:[1] FT                   /db_xref="taxon:9606"
:[1] FT                   /mol_type="mRNA"
:[1] FT                   /organism="Homo sapiens"
:[1] FT                   /dev_stage="fetus, 15-20 weeks"
:[1] FT                   /tissue_type="brain"
:[1] FT   CDS             104..2446
:[1] FT                   /db_xref="GOA:P33151"
:[1] FT                   /db_xref="SWISS-PROT:P33151"
:[1] FT                   /product="cadherin-5"
:[1] FT                   /protein_id="CAA42468.1"
:[1] FT                   
/translation="MMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQKRDW
:[1] FT                   
IWNQMHIDEEKNTSLPHHVGKIKSSVSRKNAKYLLKGEYVGKVFRVDAETGDVFAIERL
:[1] FT                   
DRENISEYHLTAVIVDKDTGENLETPSSFTIKVHDVNDNWPVFTHRLFNASVPESSAVG
:[1] FT                   
TSVISVTAVDADDPTVGDHASVMYQILKGKEYFAIDNSGRIITITKSLDREKQARYEIV
:[1] FT                   
VEARDAQGLRGDSGTATVLVTLQDINDNFPFFTQTKYTFVVPEDTRVGTSVGSLFVEDP
:[1] FT                   
DEPQNRMTKYSILRGDYQDAFTIETNPAHNEGIIKPMKPLDYEYIQQYSFIVEATDPTI
:[1] FT                   
DLRYMSPPAGNRAQVIINITDVDEPPIFQQPFYHFQLKENQKKPLIGTVLAMDPDAARH
:[1] FT                   
SIGYSIRRTSDKGQFFRVTKKGDIYNEKELDREVYPWYNLTVEAKELDSTGTPTGKESI
:[1] FT                   
VQVHIEVLDENDNAPEFAKPYQPKVCENAVHGQLVLQISAIDKDITPRNVKFKFILNTE
:[1] FT                   
NNFTLTDNHDNTANITVKYGQFDREHTKVHFLPVVISDNGMPSRTGTSTLTVAVCKCNE
:[1] FT                   
QGEFTFCEDMAAQVGVSIQAVVAILLCILTITVITLLIFLRRRLRKQARAHGKSVPEIH
:[1] FT                   
EQLVTYDEEGGGEMDTTSYDVSVLNSVRRGGAKPPRPALDARPSLYAQVQKPPRHAPGA
:[1] FT                   
HGGPGEMAAMIEVKKDEADHDGDGPPYDTLHIYGYEGSESIAESLSSLGTDSSDSDVDY
:[1] FT                   DFLNDWGPRFKMLAELYGSDPREELLY"
:[1] XX
:[1] SQ   Sequence 3170 BP; 773 A; 962 C; 844 G; 588 T; 3 other;
:[1]      ctccactcac gctcagccct ggacggacag gcagtccaac ggaacagaaa 
catccctcag        60
:[1]      cccacaggca cgatctgttc ctcctgggaa gatgcagagg ctcatgatgc 
tcctcgccac       120
:[1]      atcgggcgcc tgcctgggcc tgctggcagt ggcagcagtg gcagcagcag 
gtgctaaccc       180
:[1]      tgcccaacgg gacacccaca gcctgctgcc cacccaccgg cgccaaaaga 
gagattggat       240
:[1]      ttggaaccag atgcacattg atgaagagaa aaacacctca cttccccatc 
atgtaggcaa       300
:[1]      gatcaagtca agcgtgagtc gcaagaatgc caagtacctg ctcaaaggag 
aatatgtggg       360
:[1]      caaggtcttc cgggtcgatg cagagacagg agacgtgttc gccattgaga 
ggctggaccg       420
:[1]      ggagaatatc tcagagtacc acctcactgc tgtcattgtg gacaaggaca 
ctggcgaaaa       480
:[1]      cctggagact ccttccagct tcaccatcaa agttcatgac gtgaacgaca 
actggcctgt       540
:[1]      gttcacgcat cggttgttca atgcgtccgt gcctgagtcg tcggctgtgg 
ggacctcagt       600
:[1]      catctctgtg acagcagtgg atgcagacga ccccactgtg ggagaccacg 
cctctgtcat       660
:[1]      gtaccaaatc ctgaagggga aagagtattt tgccatcgat aattctggac 
gtattatcac       720
:[1]      aataacgaaa agcttggacc gagagaagca ggccaggtat gagatcgtgg 
tggaagcgcg       780
:[1]      agatgcccag ggcctccggg gggactcggg cacggccacc gtgctggtca 
ctctgcaaga       840
:[1]      catcaatgac aacttcccct tcttcaccca gaccaagtac acatttgtcg 
tgcctgaaga       900
:[1]      cacccgtgtg ggcacctctg tgggctctct gtttgttgag gacccagatg 
agccccagaa       960
:[1]      ccggatgacc aagtacagca tcttgcgggg cgactaccag gacgctttca 
ccattgagac      1020
:[1]      aaaccccgcc cacaacgagg gcatcatcaa gcccatgaag cctctggatt 
atgaatacat      1080
:[1]      ccagcaatac agcttcatag tcgaggccac agaccccacc atcgacctcc 
gatacatgag      1140
:[1]      ccctcccgcg ggaaacagag cccaggtcat tatcaacatc acagatgtgg 
acgagccccc      1200
:[1]      cattttccag cagcctttct accacttcca gctgaaggaa aaccagaaga 
agcctctgat      1260
:[1]      tggcacagtg ctggccatgg accctgatgc ggctaggcat agcattggat 
actccatccg      1320
:[1]      caggaccagt gacaagggcc agttcttccg agtcacaaaa aagggggaca 
tttacaatga      1380
:[1]      gaaagaactg gacagagaag tctacccctg gtataacctg actgtggagg 
ccaaagaact      1440
:[1]      ggattccact ggaaccccca caggaaaaga atccattgtg caagtccaca 
ttgaagtttt      1500
:[1]      ggatgagaat gacaatgccc cggagtttgc caagccctac cagcccaaag 
tgtgtgagaa      1560
:[1]      cgctgtccat ggccagctgg tcctgcagat ctccgcaata gacaaggaca 
taacaccacg      1620
:[1]      aaacgtgaag ttcaaattca tcttgaatac tgagaacaac tttaccctca 
cggataatca      1680
:[1]      cgataacacg gccaacatca cagtcaagta tgggcagttt gaccgggagc 
ataccaaggt      1740
:[1]      ccacttccta cccgtggtca tctcagacaa tgggatgcca agtcgcacgg 
gcaccagcac      1800
:[1]      gctgaccgtg gccgtgtgca agtgcaacga gcagggcgag ttcaccttct 
gcgaggatat      1860
:[1]      ggccgcccag gtgggcgtga gcatccaggc agtggtagcc atcttactct 
gcatcctcac      1920
:[1]      catcacagtg atcaccctgc tcatcttcct gcggcggcgg ctccggaagc 
aggcccgcgc      1980
:[1]      gcacggcaag agcgtgccgg agatccacga gcagctggtc acctacgacg 
aggagggcgg      2040
:[1]      cggcgagatg gacaccacca gctacgatgt gtcggtgctc aactcggtgc 
gccgcggcgg      2100
:[1]      ggccaagccc ccgcggcccg cgctggacgc ccggccttcc ctctatgcgc 
aggtgcagaa      2160
:[1]      gccaccgagg cacgcgcctg gggcacacgg agggcccggg gagatggcag 
ccatgatcga      2220
:[1]      ggtgaagaag gacgaggcgg accacgacgg cgacggcccc ccctacgaca 
cgctgcacat      2280
:[1]      ctacggctac gagggctccg agtccatagc cgagtccctc agctccctgg 
gcaccgactc      2340
:[1]      atccgactct gacgtggatt acgacttcct taacgactgg ggacccaggt 
ttaagatgct      2400
:[1]      ggctgagctg tacggctcgg acccccggga ggagctgctg tattaggcgg 
ccgaggtcac      2460
:[1]      tctgggcctg gggacccaaa ccccctgcag cccaggccag tcagactcca 
ggcaccacag      2520
:[1]      cvncadctcc aaaaatggca gtgactcccc agcccagcac cccttcctcg 
tgggtcccag      2580
:[1]      agacctcatc agccttggga tagcaaactc caggttcctg aaatatccag 
gaatatatgt      2640
:[1]      cagtgatgac tattctcaaa tgctggcaaa tccaggctgg tgttctgtct 
gggctcagac      2700
:[1]      atccacataa ccctgtcacc cacagaccgc cgtctaactc aaagacttcc 
tctggctccc      2760
:[1]      caaggctgca aagcaaaaca gactgtgttt aactgctgca gggtcttttt 
ctagggtccc      2820
:[1]      tgaacgccct ggtaaggctg gtgaggtcct ggtgcctatc tgcctggagg 
caaaggcctg      2880
:[1]      gacagcttga cttgtggggc aggattctct gcagcccatt cccaagggag 
actgaccatc      2940
:[1]      atgccctctc tcgggagccc tagccctgct ccaactccat actccactcc 
aagtgcccca      3000
:[1]      ccactcccca acccctctcc aggcctgtca agagggagga aggggcccca 
tggcagctcc      3060
:[1]      tgaccttggg tcctgaagtg acctcactgg cctgccatgc cagtaactgt 
gctgtactga      3120
:[1]      gcactgaacc acattcaggg aaatggctta ttaaactttg aagcaactgt        
          3170
:[1] //
ajRegFree 1b27a0 size regexp 4
ajRegFree 1b2890 size regexp 4
ajRegFree 1b2960 size regexp 4
ajRegFree 1b29e0 size regexp 4
ajRegFree 1b2a80 size regexp 4
ajRegFree 1afa60 size regexp 4
ajRegFree 1afb30 size regexp 4
ajRegFree 1afbc0 size regexp 4
ajRegFree 1afc50 size regexp 4
seqRead: seqin format 3 'embl'
ajFeattableDel 0
seqRead: cleared
seqRead: one format specified
ajFileBuffNoBuff  buffsize: 132
++seqRead known format 3
++seqReadFmt format 3 (embl) 'qasrswww:HSCAD5' feat No
seqReadEmbl first line 'Date: Sat, 29 Nov 2003 09:46:49 GMT
'
Format 3 (embl) failed, file buffer reset by seqReadFmt
++seqReadFmt failed - nothing read
seqRead: (b2) seqReadFmt stat == FAIL *failed*
ajFeattableDel 0
seqRead failed - try again with format 3 'embl'
++seqReadFmt format 3 (embl) 'qasrswww:HSCAD5' feat No
seqReadEmbl first line 'Date: Sat, 29 Nov 2003 09:46:49 GMT
'
Format 3 (embl) failed, file buffer reset by seqReadFmt
++seqReadFmt failed - nothing read
seqRead: (b3) seqReadFmt stat == FAIL *failed*
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