problem with dbifasta and long files?

[Martin Sarachu]

Hi,

I'm having an "cannot read" error when trying to index with dbifasta.
Here is the output

> $ ls -lsa
> .
> .
> .
> 5894336 -rw-r--r--   1 martin   6032840325 Jun 15 17:10 nt
> .

> $ dbifasta -debug
> Index a fasta database
>     simple : >ID
>      idacc : >ID ACC
>      gcgid : >db:ID
>   gcgidacc : >db:ID ACC
>       dbid : >db ID
>       ncbi : | formats
> ID line format [idacc]: ncbi
> Database directory [.]: 
> Wildcard database filename [*.dat]: nt
> Database name: nt
> Release number [0.0]: 
> Index date [00/00/00]: 
> 
>    EMBOSS An error in embdbi.c at line 295:
> Cannot open ./nt for reading
>
> $

I'm also sending dbifasta.dbg just in case

martin

-- 
Martin Sarachu
mad at biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org
-------------- next part --------------
acdArgsScan acdDebug Yes acdDoHelp No
ajFileNewIn '/usr/local/EMBOSS/share/EMBOSS/acd/dbifasta.acd'
ajNamResolve of '/usr/local/EMBOSS/share/EMBOSS/acd/dbifasta.acd'
EOF ajFileGetsL file /usr/local/EMBOSS/share/EMBOSS/acd/dbifasta.acd
closing file '/usr/local/EMBOSS/share/EMBOSS/acd/dbifasta.acd'
acdSetDefC auto 'N' 2bec8
acdSetDefC stdout 'N' 2bf68
acdSetDefC filter 'N' 2c008
acdSetDefC options 'N' 2c0a8
acdSetDefC debug 'N' 2c148
acdSetDefC acdlog 'N' 2c1e8
acdSetDefC acdpretty 'N' 2c288
acdSetDefC acdtable 'N' 2c328
acdSetDefC help 'N' 2c3c8
acdSetDefC verbose 'N' 2c468
acdSetDefC warning 'Y' 2c508
acdSetDefC error 'Y' 2c5a8
acdSetDefC fatal 'Y' 2c648
acdSetDefC die 'N' 2cf60
acdSetVarDef today '16/06/02' ff2650cc
acdNewSec 'input' acdSecList length 0
acdNewSec acdSecList push 'input' new length 1
acdSet attr 'idformat' val 'required' type ''
acdSet attr 'idformat' val 'information' type ''
acdSet attr 'idformat' val 'values' type ''
acdSet attr 'idformat' val 'maximum' type ''
acdSet attr 'idformat' val 'minimum' type ''
acdSet attr 'idformat' val 'default' type ''
acdSet attr 'idformat' val 'delimiter' type ''
acdSet attr 'idformat' val 'codedelimiter' type ''
acdSet attr 'directory' val 'required' type ''
acdSet attr 'directory' val 'default' type ''
acdSet attr 'directory' val 'information' type ''
acdSet attr 'filenames' val 'required' type ''
acdSet attr 'filenames' val 'default' type ''
acdSet attr 'filenames' val 'information' type ''
acdNewEndsec 'input' acdSecList length 1
Pop from acdSecList 'input' new length 0
acdNewSec 'required' acdSecList length 0
acdNewSec acdSecList push 'required' new length 1
acdSet attr 'dbname' val 'parameter' type ''
acdSet attr 'dbname' val 'maxlength' type ''
acdSet attr 'dbname' val 'minlength' type ''
acdSet attr 'dbname' val 'information' type ''
acdSet attr 'release' val 'required' type ''
acdSet attr 'release' val 'default' type ''
acdSet attr 'release' val 'maxlength' type ''
acdSet attr 'release' val 'information' type ''
acdSet attr 'date' val 'required' type ''
acdSet attr 'date' val 'default' type ''
acdSet attr 'date' val 'valid' type ''
acdSet attr 'date' val 'information' type ''
acdSet attr 'date' val 'pattern' type ''
acdNewEndsec 'required' acdSecList length 1
Pop from acdSecList 'required' new length 0
acdNewSec 'advanced' acdSecList length 0
acdNewSec acdSecList push 'advanced' new length 1
acdSet attr 'fields' val 'required' type ''
acdSet attr 'fields' val 'information' type ''
acdSet attr 'fields' val 'values' type ''
acdSet attr 'fields' val 'minimum' type ''
acdSet attr 'fields' val 'maximum' type ''
acdSet attr 'fields' val 'default' type ''
acdSet attr 'exclude' val 'information' type ''
acdSet attr 'indexdirectory' val 'default' type ''
acdSet attr 'indexdirectory' val 'information' type ''
acdSet attr 'maxindex' val 'default' type ''
acdSet attr 'maxindex' val 'minimum' type ''
acdSet attr 'maxindex' val 'information' type ''
acdSet attr 'sortoptions' val 'default' type ''
acdSet attr 'sortoptions' val 'information' type ''
acdSet attr 'sortoptions' val 'help' type ''
acdSet attr 'systemsort' val 'default' type ''
acdSet attr 'systemsort' val 'information' type ''
acdSet attr 'cleanup' val 'default' type ''
acdSet attr 'cleanup' val 'information' type ''
acdNewEndsec 'advanced' acdSecList length 1
Pop from acdSecList 'advanced' new length 0
-- All Done : acdSecList length 0
acdSet attr 'dbname' val 'required' type ''
acdDef debug 'Y' 2c148
acdSetDef debug 'Y' 2c148
acdSetBool -auto def: N
acdSetQualAppl 'auto'
acdSetBool -auto val: No
acdSetBool -stdout def: N
acdSetQualAppl 'stdout'
acdSetBool -stdout val: No
acdSetBool -filter def: N
acdSetQualAppl 'filter'
acdSetBool -filter val: No
acdSetBool -options def: N
acdSetQualAppl 'options'
acdSetBool -options val: No
acdSetBool -debug def: Y
acdSetQualAppl 'debug'
acdSetBool -debug val: Yes
acdSetBool -acdlog def: N
acdSetQualAppl 'acdlog'
acdSetBool -acdlog val: No
acdSetBool -acdpretty def: N
acdSetQualAppl 'acdpretty'
acdSetBool -acdpretty val: No
acdSetBool -acdtable def: N
acdSetQualAppl 'acdtable'
acdSetBool -acdtable val: No
acdSetBool -help def: N
acdSetQualAppl 'help'
acdSetBool -help val: No
acdHelp No
acdSetBool -verbose def: N
acdSetQualAppl 'verbose'
acdSetBool -verbose val: No
acdSetBool -warning def: Y
acdSetQualAppl 'warning'
acdSetBool -warning val: Yes
acdSetBool -error def: Y
acdSetQualAppl 'error'
acdSetBool -error val: Yes
acdSetBool -fatal def: Y
acdSetQualAppl 'fatal'
acdSetBool -fatal val: Yes
acdSetBool -die def: N
acdSetQualAppl 'die'
acdSetBool -die val: No
acdUserGet 'idformat' reply 'idacc'
acdUserGet 'idformat' defreply 'idacc' msg 'ID line format'
ajUserGet buffer len: 5 res: 2048 ptr: 30bc8
testing 'ncbi'
Found 1 matches OK: Y min: 1 max: 1
Accept: 'ncbi'
Found 1 matches
Menu length now 0
before return val[0] 'ncbi'
before return val[0] 'ncbi'
Storing val[0] 'ncbi'
acdUserGet 'directory' reply '.'
acdUserGet 'directory' defreply '.' msg 'Database directory'
ajUserGet buffer len: 1 res: 2048 ptr: 31418
acdUserGet 'filenames' reply '*.dat'
acdUserGet 'filenames' defreply '*.dat' msg 'Wildcard database filename'
ajUserGet buffer len: 5 res: 2048 ptr: 31418
acdUserGet 'dbname' reply ''
acdUserGet 'dbname' defreply '' msg 'Database name'
ajUserGet buffer len: 0 res: 2048 ptr: 31418
acdUserGet 'release' reply '0.0'
acdUserGet 'release' defreply '0.0' msg 'Release number'
ajUserGet buffer len: 3 res: 2048 ptr: 31418
acdUserGet 'date' reply '00/00/00'
acdUserGet 'date' defreply '00/00/00' msg 'Index date'
ajUserGet buffer len: 8 res: 2048 ptr: 31418
testing 'acnum'
Found 1 matches OK: Y min: 0 max: 5
Accept: 'acnum'
Found 1 matches
Menu length now 0
before return val[0] 'acnum'
before return val[0] 'acnum'
Storing val[0] 'acnum'
acdSetBool -systemsort def: Y
acdSetQualAppl 'systemsort'
acdSetBool -systemsort val: Yes
acdSetBool -cleanup def: Y
acdSetQualAppl 'cleanup'
acdSetBool -cleanup val: Yes
reading './nt'
writing './'
embDbiFileListExc dir '.' wildfile 'nt' exclude ''
dirfix './'
ajFileTestSkip: file '.' exclude: '' include: 'nt'
ajFileTestSkip: file '..' exclude: '' include: 'nt'
ajFileTestSkip: file 'update.log' exclude: '' include: 'nt'
ajFileTestSkip: file 'README' exclude: '' include: 'nt'
ajFileTestSkip: file 'update.error' exclude: '' include: 'nt'
ajFileTestSkip: file 'release.error' exclude: '' include: 'nt'
ajFileTestSkip: file 'release.log' exclude: '' include: 'nt'
ajFileTestSkip: file 'nt' exclude: '' include: 'nt'
ajFileTestSkip: file 'nt' included by 'nt'
accept 'nt'
ajFileTestSkip: file 'fmerge.log' exclude: '' include: 'nt'
ajFileTestSkip: file 'dbifasta.dbg' exclude: '' include: 'nt'
ajFileTestSkip: file 'index.nr' exclude: '' include: 'nt'
ajFileTestSkip: file 'division.lkp' exclude: '' include: 'nt'
ajFileTestSkip: file 'entrynam.idx' exclude: '' include: 'nt'
ajFileTestSkip: file 'acnum.trg' exclude: '' include: 'nt'
ajFileTestSkip: file 'acnum.hit' exclude: '' include: 'nt'
1 files for '.' 'nt'
ajFileNewIn './nt'
ajNamResolve of './nt'