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Old 02-01-2012, 05:22 PM   #1
detq182
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Default Makeblastdb problem

i just download a secuence in .FASTA format from uniprot but
i cant make it work, this are the errors.

makeblastdb -in Arabidopsis_thaliana.fas -parse_seqids -dbtype prot
BLAST Database error: No alias or index file found for protein database [Arabido
psis_thaliana.fas] in search path [C:\blast-2.2.25+;C:\blast-2.2.25+\db;]

makeblastdb -in swissprot.fas -dbtype prot -out Thaliana
Error: Unable to open input swissprot.fas as either FASTA file or BLAST db

makeblastdb -in swissprot.fas -dbtype prot -out Thaliana.db
Error: Unable to open input swissprot.fas as either FASTA file or BLAST db

Please help......
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Old 02-01-2012, 06:20 PM   #2
Kennels
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check your downloaded sequences for whether they are truly in fasta format. the errors are complaining that it isn't
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Old 02-02-2012, 01:55 AM   #3
detq182
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thanks Kennels, but how can i check it ? the downloaded sequences said Arabidopsis_thaliana.Protein.fasta
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Old 02-02-2012, 03:52 AM   #4
Kennels
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On the command line, type

Code:
head -n 4 <name of your fasta file>
what do the headers and sequence look like?
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Old 02-02-2012, 04:01 AM   #5
GenoMax
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It appears that detq182 is doing this on a windows machine.

@detq182: Are you using cygwin to do this or natively in windows itself?
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Old 02-02-2012, 05:28 AM   #6
detq182
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Quote:
Originally Posted by Kennels View Post
On the command line, type

Code:
head -n 4 <name of your fasta file>
what do the headers and sequence look like?
Cant do the command line. head command dont recognise.
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Old 02-02-2012, 05:31 AM   #7
detq182
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Quote:
Originally Posted by GenoMax View Post
It appears that detq182 is doing this on a windows machine.

@detq182: Are you using cygwin to do this or natively in windows itself?
Yes im on windows and natively not using cygwin.

please help.....
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Old 02-02-2012, 01:33 PM   #8
detq182
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I finally can do it

comman line:
makeblastdb -in \blast-2.2.25+\db\uniprot_sprot.fasta -parse_seqids -dbtype prot

and done, thank all of you for your time.
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Old 03-17-2014, 01:49 AM   #9
jp.
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Question

Hi
Can someone please explain me how to make blast database in details.
I have downloaded the following dir and kept under wd:
1. wd/ncbi-blast-2.2.29+
2. wdblast
3. wd/blast/nr
4. wd/blast/nt
5. wd/blast/other genomic

I get the error:
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nr]
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nt]
thank you
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Old 03-17-2014, 04:14 AM   #10
GenoMax
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It is not clear if you have downloaded the pre-made indexes for nr/nt etc from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) though you made the directory structure above.
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Old 03-17-2014, 06:00 AM   #11
jp.
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Yes, I have downloaded from there only all the database.
But the problem is that I dont know how to make database, the files are there in the exact PATH but program can not find it cos database is prepared and balst is not installed so blast can not read these files , thats my problem...
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Old 03-17-2014, 06:09 AM   #12
GenoMax
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Quote:
Originally Posted by jp. View Post
Yes, I have downloaded from there only all the database.
But the problem is that I dont know how to make database, the files are there in the exact PATH but program can not find it cos database is prepared and balst is not installed so blast can not read these files , thats my problem...
Forgive me if the following is redundant but I am not clear about what you are trying to say above.

The blast executables are available here: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/2.2.29/ Get the one that is appropriate for your OS. Once those are uncompressed you should be good to go forward.
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Old 03-17-2014, 11:54 PM   #13
jp.
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I m sorry for not mentioning exactly before. The blast executable was downloaded from here only: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/2.2.29/ for linux64 bit. However, I dont have problem in blast executables. and the database for blast (such as nr, nt, other genomic) were ftp://ftp.ncbi.nlm.nih.gov/blast/db/

The problem is, while running the blast, it can not read the database files (nr, nt, other genomics) in the PATH (./blast/nr, ./blast/nt, ./blast). Eventhough, these files are at same PATH but blast executable can not read it and give error stating that can not find these files in the following PATH (./blast/nr, ./blast/nt, ./blast). Because, I think, I did not generated blast databse using blast+/2.2.29/bin/.. commands. I think, I need to make database and then indexes (but I think, I downloaded pre-built indexes) and do something that blast+/2.2.29/ can read the database files...
????
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Old 03-18-2014, 03:02 AM   #14
mastal
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If you have downloaded pre-built databases, then you don't need to make a database.

Have a look at the blast manual:

http://www.ncbi.nlm.nih.gov/books/NBK1763/

You need to set a variable BLASTDB with the path to the blast databases,
or else specify the complete path to the database, starting from the root directory.
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Old 03-18-2014, 07:00 PM   #15
jp.
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I think so that pre-built db needs only PATH. and I did as follows:
dir structure
PATH=$PATH:wd/ncbi-blast-2.2.29+/bin
PATH=$PATH:wd/blast
PATH=$PATH:wd/blast/nr
PATH=$PATH:wd/blast/nt
PATH=$PATH:wd/blast
I get the error:
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nr]
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nt]

that is my problem...????
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Old 03-19-2014, 02:57 AM   #16
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What is the command you are using to run blast?
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Old 03-19-2014, 03:04 AM   #17
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quote from the blast manual:

"the application will search for the file in the following order and locations:

1. Current working directory
2. User's HOME directory
3. Directory specified by the NCBI environment variable

The search for this file will stop at the first location where it is found and the configurations settings from that file will be applied. If the configuration file is not found, default values will apply. The following are the possible configuration parameters that impact the BLAST+ applications:


Configuration Parameter Specifies Default value
BLASTDB Path to BLAST databases. Current working directory"
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Old 03-19-2014, 03:24 AM   #18
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Did you make sure that there are read permissions available for the wd/blast/nt (and nr) directory files to which ever account you are using to run the blast search?

If the read permissions are correct then in addition to what Maria has asked for please post a listing of the files in wd/blast/nt.

Code:
$ ls -l /path_to/wd/blast/nt
Code:
$ ls -l /path_to/wd/blast/nr
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Old 03-19-2014, 04:55 PM   #19
jp.
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Let me thank u first, and read permissions are:
$ pwd
$ ./wd
$ ls -l ./wd/blast
total 4328832
-rwxrwxr-x 1 jp jp 43599965 Jan 15 15:37 ensGene.txt
-rwxrwxr-x 1 jp jp 1078 Jan 15 15:37 human_genomic.12.nhd
-rwxrwxr-x 1 jp jp 88 Jan 15 15:37 human_genomic.12.nhi
-rwxrwxr-x 1 jp jp 16068 Jan 15 15:37 human_genomic.12.nhr
-rwxrwxr-x 1 jp jp 1048 Jan 15 15:37 human_genomic.12.nin
-rwxrwxr-x 1 jp jp 824 Jan 15 15:37 human_genomic.12.nnd
-rwxrwxr-x 1 jp jp 52 Jan 15 15:37 human_genomic.12.nni
-rwxrwxr-x 1 jp jp 348 Jan 15 15:37 human_genomic.12.nog
-rwxrwxr-x 1 jp jp 2710 Jan 15 15:37 human_genomic.12.nsd
-rwxrwxr-x 1 jp jp 124 Jan 15 15:37 human_genomic.12.nsi
-rwxrwxr-x 1 jp jp 113325568 Jan 15 15:37 human_genomic.12.nsq
-rwxrwxr-x 1 jp jp 406940 Jan 15 15:37 mcl
drwxrwxr-x 2 jp jp 8192 Mar 17 14:54 nr
drwxrwxr-x 2 jp jp 4096 Mar 17 14:54 nt
-rwxrwxr-x 1 jp jp 22091585 Jan 15 15:37 nt.15.nhd
-rwxrwxr-x 1 jp jp 500366 Jan 15 15:37 nt.15.nhi
-rwxrwxr-x 1 jp jp 218076088 Jan 15 15:37 nt.15.nhr
-rwxrwxr-x 1 jp jp 14882864 Jan 15 15:37 nt.15.nin
-rwxrwxr-x 1 jp jp 10164224 Jan 15 15:37 nt.15.nnd
-rwxrwxr-x 1 jp jp 39748 Jan 15 15:37 nt.15.nni
-rwxrwxr-x 1 jp jp 4960956 Jan 15 15:37 nt.15.nog
-rwxrwxr-x 1 jp jp 48620365 Jan 15 15:37 nt.15.nsd
-rwxrwxr-x 1 jp jp 1115893 Jan 15 15:37 nt.15.nsi
-rwxrwxr-x 1 jp jp 60005376 Jan 15 15:37 nt.15.nsq
-rwxrwxr-x 1 jp jp 13616 Jan 15 15:37 other_genomic.50.nhd
-rwxrwxr-x 1 jp jp 384 Jan 15 15:37 other_genomic.50.nhi
-rwxrwxr-x 1 jp jp 155395 Jan 15 15:37 other_genomic.50.nhr
-rwxrwxr-x 1 jp jp 11284 Jan 15 15:37 other_genomic.50.nin
-rwxrwxr-x 1 jp jp 7488 Jan 15 15:37 other_genomic.50.nnd
-rwxrwxr-x 1 jp jp 76 Jan 15 15:37 other_genomic.50.nni
-rwxrwxr-x 1 jp jp 3760 Jan 15 15:37 other_genomic.50.nog
-rwxrwxr-x 1 jp jp 26324 Jan 15 15:37 other_genomic.50.nsd
-rwxrwxr-x 1 jp jp 677 Jan 15 15:37 other_genomic.50.nsi
-rwxrwxr-x 1 jp jp 86990336 Jan 15 15:37 other_genomic.50.nsq
-rwxrwxr-x 1 jp jp 13135052 Jan 15 15:37 refGene.txt
-rwxrwxr-x 1 jp jp 3794465994 Jan 15 15:37 tophat_Calu3.tar.gz
$ ls -l ./wd/blast/nr
total 36017072
-rw-r--r-- 1 jp jp 15721799 Jul 26 2013 nr.00.phd
-rw-r--r-- 1 jp jp 356928 Jul 26 2013 nr.00.phi
-rw-rw-r-- 1 jp jp 1243954497 Jul 29 2013 nr.00.phr
-rw-rw-r-- 1 jp jp 7118816 Jul 29 2013 nr.00.pin
-rw-rw-r-- 1 jp jp 66841544 Jul 29 2013 nr.00.pnd
-rw-rw-r-- 1 jp jp 261148 Jul 29 2013 nr.00.pni
-rw-r--r-- 1 jp jp 3559352 Jul 28 2013 nr.00.pog
-rw-rw-r-- 1 jp jp 7118640 Jul 26 2013 nr.00.ppd
-rw-rw-r-- 1 jp jp 27852 Jul 26 2013 nr.00.ppi
-rw-rw-r-- 1 jp jp 289897508 Jul 29 2013 nr.00.psd
-rw-rw-r-- 1 jp jp 6668144 Jul 29 2013 nr.00.psi
-rw-rw-r-- 1 jp jp 311715428 Jul 26 2013 nr.00.psq
-rwxrwxr-x 1 jp jp 511421044 Jan 15 15:36 nr.00.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.00.tar.gz.md5
-rw-r--r-- 1 jp jp 45838159 Jul 25 2013 nr.01.phd
-rw-r--r-- 1 jp jp 1029258 Jul 25 2013 nr.01.phi
-rw-rw-r-- 1 jp jp 1014893828 Jul 29 2013 nr.01.phr
-rw-rw-r-- 1 jp jp 20040808 Jul 29 2013 nr.01.pin
-rw-rw-r-- 1 jp jp 55016544 Jul 29 2013 nr.01.pnd
-rw-rw-r-- 1 jp jp 214956 Jul 29 2013 nr.01.pni
-rw-r--r-- 1 jp jp 10020348 Jul 28 2013 nr.01.pog
-rw-rw-r-- 1 jp jp 20040632 Jul 25 2013 nr.01.ppd
-rw-rw-r-- 1 jp jp 78332 Jul 25 2013 nr.01.ppi
-rw-rw-r-- 1 jp jp 263119885 Jul 29 2013 nr.01.psd
-rw-rw-r-- 1 jp jp 5813333 Jul 29 2013 nr.01.psi
-rw-rw-r-- 1 jp jp 857285124 Jul 25 2013 nr.01.psq
-rwxrwxr-x 1 jp jp 734911695 Jan 15 15:36 nr.01.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.01.tar.gz.md5
-rw-r--r-- 1 jp jp 50070578 Jul 26 2013 nr.02.phd
-rw-r--r-- 1 jp jp 1123685 Jul 26 2013 nr.02.phi
-rw-rw-r-- 1 jp jp 1265588335 Jul 29 2013 nr.02.phr
-rw-rw-r-- 1 jp jp 21848560 Jul 29 2013 nr.02.pin
-rw-rw-r-- 1 jp jp 66975832 Jul 29 2013 nr.02.pnd
-rw-rw-r-- 1 jp jp 261676 Jul 29 2013 nr.02.pni
-rw-r--r-- 1 jp jp 10924224 Jul 28 2013 nr.02.pog
-rw-rw-r-- 1 jp jp 21848384 Jul 26 2013 nr.02.ppd
-rw-rw-r-- 1 jp jp 85396 Jul 26 2013 nr.02.ppi
-rw-rw-r-- 1 jp jp 319724556 Jul 29 2013 nr.02.psd
-rw-rw-r-- 1 jp jp 7072940 Jul 29 2013 nr.02.psi
-rw-rw-r-- 1 jp jp 931075490 Jul 26 2013 nr.02.psq
-rwxrwxr-x 1 jp jp 801648368 Jan 15 15:36 nr.02.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.02.tar.gz.md5
-rw-r--r-- 1 jp jp 52748192 Jul 22 2013 nr.03.phd
-rw-r--r-- 1 jp jp 1183412 Jul 22 2013 nr.03.phi
-rw-r--r-- 1 jp jp 1262229768 Jul 29 2013 nr.03.phr
-rw-r--r-- 1 jp jp 22990728 Jul 29 2013 nr.03.pin
-rw-r--r-- 1 jp jp 67514512 Jul 29 2013 nr.03.pnd
-rw-r--r-- 1 jp jp 263780 Jul 29 2013 nr.03.pni
-rw-r--r-- 1 jp jp 11495308 Jul 28 2013 nr.03.pog
-rw-r--r-- 1 jp jp 22990552 Jul 22 2013 nr.03.ppd
-rw-r--r-- 1 jp jp 89852 Jul 22 2013 nr.03.ppi
-rw-r--r-- 1 jp jp 325282606 Jul 29 2013 nr.03.psd
-rw-r--r-- 1 jp jp 7259801 Jul 29 2013 nr.03.psi
-rw-r--r-- 1 jp jp 959596718 Jul 22 2013 nr.03.psq
-rwxrwxr-x 1 jp jp 821576451 Jan 15 15:37 nr.03.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.03.tar.gz.md5
-rw-r--r-- 1 jp jp 48668815 Jul 27 2013 nr.04.phd
-rw-r--r-- 1 jp jp 1092479 Jul 27 2013 nr.04.phi
-rw-r--r-- 1 jp jp 999766178 Jul 29 2013 nr.04.phr
-rw-r--r-- 1 jp jp 21249736 Jul 29 2013 nr.04.pin
-rw-r--r-- 1 jp jp 53232792 Jul 29 2013 nr.04.pnd
-rw-r--r-- 1 jp jp 207988 Jul 29 2013 nr.04.pni
-rw-r--r-- 1 jp jp 10624812 Jul 28 2013 nr.04.pog
-rw-r--r-- 1 jp jp 21249560 Jul 27 2013 nr.04.ppd
-rw-r--r-- 1 jp jp 83052 Jul 27 2013 nr.04.ppi
-rw-r--r-- 1 jp jp 256882530 Jul 29 2013 nr.04.psd
-rw-r--r-- 1 jp jp 5574883 Jul 29 2013 nr.04.psi
-rw-r--r-- 1 jp jp 950506467 Jul 27 2013 nr.04.psq
-rwxrwxr-x 1 jp jp 761672464 Jan 15 15:37 nr.04.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.04.tar.gz.md5
-rw-r--r-- 1 jp jp 50416439 Jul 27 2013 nr.05.phd
-rw-r--r-- 1 jp jp 1131689 Jul 27 2013 nr.05.phi
-rw-r--r-- 1 jp jp 899567213 Jul 29 2013 nr.05.phr
-rw-r--r-- 1 jp jp 21995864 Jul 29 2013 nr.05.pin
-rw-r--r-- 1 jp jp 47845000 Jul 29 2013 nr.05.pnd
-rw-r--r-- 1 jp jp 186940 Jul 29 2013 nr.05.pni
-rw-r--r-- 1 jp jp 10997876 Jul 27 2013 nr.05.pog
-rw-r--r-- 1 jp jp 21995688 Jul 27 2013 nr.05.ppd
-rw-r--r-- 1 jp jp 85972 Jul 27 2013 nr.05.ppi
-rw-r--r-- 1 jp jp 232308885 Jul 29 2013 nr.05.psd
-rw-r--r-- 1 jp jp 5188612 Jul 29 2013 nr.05.psi
-rw-r--r-- 1 jp jp 979481471 Jul 27 2013 nr.05.psq
-rwxrwxr-x 1 jp jp 763862888 Jan 15 15:37 nr.05.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.05.tar.gz.md5
-rw-r--r-- 1 jp jp 53201065 Jul 27 2013 nr.06.phd
-rw-r--r-- 1 jp jp 1193537 Jul 27 2013 nr.06.phi
-rw-r--r-- 1 jp jp 989783176 Jul 29 2013 nr.06.phr
-rw-r--r-- 1 jp jp 23183952 Jul 29 2013 nr.06.pin
-rw-r--r-- 1 jp jp 53054520 Jul 29 2013 nr.06.pnd
-rw-r--r-- 1 jp jp 207292 Jul 29 2013 nr.06.pni
-rw-r--r-- 1 jp jp 11591920 Jul 27 2013 nr.06.pog
-rw-r--r-- 1 jp jp 23183776 Jul 27 2013 nr.06.ppd
-rw-r--r-- 1 jp jp 90612 Jul 27 2013 nr.06.ppi
-rw-r--r-- 1 jp jp 256887778 Jul 29 2013 nr.06.psd
-rw-r--r-- 1 jp jp 5614161 Jul 29 2013 nr.06.psi
-rw-r--r-- 1 jp jp 972339454 Jul 27 2013 nr.06.psq
-rwxrwxr-x 1 jp jp 782883610 Jan 15 15:37 nr.06.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.06.tar.gz.md5
-rw-r--r-- 1 jp jp 44331006 Jul 23 2013 nr.07.phd
-rw-r--r-- 1 jp jp 995657 Jul 23 2013 nr.07.phi
-rw-r--r-- 1 jp jp 737273452 Jul 29 2013 nr.07.phr
-rw-r--r-- 1 jp jp 19398176 Jul 29 2013 nr.07.pin
-rw-r--r-- 1 jp jp 39588744 Jul 29 2013 nr.07.pnd
-rw-r--r-- 1 jp jp 154692 Jul 29 2013 nr.07.pni
-rw-r--r-- 1 jp jp 9699032 Jul 26 2013 nr.07.pog
-rw-r--r-- 1 jp jp 19398000 Jul 23 2013 nr.07.ppd
-rw-r--r-- 1 jp jp 75820 Jul 23 2013 nr.07.ppi
-rw-r--r-- 1 jp jp 190282313 Jul 29 2013 nr.07.psd
-rw-r--r-- 1 jp jp 4190752 Jul 29 2013 nr.07.psi
-rw-r--r-- 1 jp jp 835692590 Jul 23 2013 nr.07.psq
-rwxrwxr-x 1 jp jp 654732603 Jan 15 15:37 nr.07.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.07.tar.gz.md5
-rw-r--r-- 1 jp jp 29569263 Jul 22 2013 nr.08.phd
-rw-r--r-- 1 jp jp 667013 Jul 22 2013 nr.08.phi
-rw-r--r-- 1 jp jp 1272421576 Jul 29 2013 nr.08.phr
-rw-r--r-- 1 jp jp 13116568 Jul 29 2013 nr.08.pin
-rw-r--r-- 1 jp jp 67398424 Jul 29 2013 nr.08.pnd
-rw-r--r-- 1 jp jp 263324 Jul 29 2013 nr.08.pni
-rw-r--r-- 1 jp jp 6558228 Jul 28 2013 nr.08.pog
-rw-r--r-- 1 jp jp 13116392 Jul 22 2013 nr.08.ppd
-rw-r--r-- 1 jp jp 51284 Jul 22 2013 nr.08.ppi
-rw-r--r-- 1 jp jp 306885543 Jul 29 2013 nr.08.psd
-rw-r--r-- 1 jp jp 6967481 Jul 29 2013 nr.08.psi
-rw-r--r-- 1 jp jp 537197406 Jul 22 2013 nr.08.psq
-rwxrwxr-x 1 jp jp 654067415 Jan 15 15:37 nr.08.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.08.tar.gz.md5
-rw-r--r-- 1 jp jp 51194387 Jul 25 2013 nr.09.phd
-rw-r--r-- 1 jp jp 1148977 Jul 25 2013 nr.09.phi
-rw-r--r-- 1 jp jp 832163992 Jul 29 2013 nr.09.phr
-rw-r--r-- 1 jp jp 22328336 Jul 29 2013 nr.09.pin
-rw-r--r-- 1 jp jp 43976832 Jul 29 2013 nr.09.pnd
-rw-r--r-- 1 jp jp 171836 Jul 29 2013 nr.09.pni
-rw-r--r-- 1 jp jp 11164112 Jul 27 2013 nr.09.pog
-rw-r--r-- 1 jp jp 22328160 Jul 25 2013 nr.09.ppd
-rw-r--r-- 1 jp jp 87268 Jul 25 2013 nr.09.ppi
-rw-r--r-- 1 jp jp 213351481 Jul 29 2013 nr.09.psd
-rw-r--r-- 1 jp jp 4690669 Jul 29 2013 nr.09.psi
-rw-r--r-- 1 jp jp 1004903172 Jul 25 2013 nr.09.psq
-rwxrwxr-x 1 jp jp 750006901 Jan 15 15:37 nr.09.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.09.tar.gz.md5
-rw-r--r-- 1 jp jp 46048845 Jul 27 2013 nr.10.phd
-rw-r--r-- 1 jp jp 1034156 Jul 27 2013 nr.10.phi
-rw-r--r-- 1 jp jp 731547101 Jul 29 2013 nr.10.phr
-rw-r--r-- 1 jp jp 20131368 Jul 29 2013 nr.10.pin
-rw-r--r-- 1 jp jp 38668768 Jul 29 2013 nr.10.pnd
-rw-r--r-- 1 jp jp 151100 Jul 29 2013 nr.10.pni
-rw-r--r-- 1 jp jp 10065628 Jul 28 2013 nr.10.pog
-rw-r--r-- 1 jp jp 20131192 Jul 27 2013 nr.10.ppd
-rw-r--r-- 1 jp jp 78684 Jul 27 2013 nr.10.ppi
-rw-r--r-- 1 jp jp 187736701 Jul 29 2013 nr.10.psd
-rw-r--r-- 1 jp jp 4127109 Jul 29 2013 nr.10.psi
-rw-r--r-- 1 jp jp 984295947 Jul 27 2013 nr.10.psq
-rwxrwxr-x 1 jp jp 692293957 Jan 15 15:37 nr.10.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.10.tar.gz.md5
-rw-r--r-- 1 jp jp 53938987 Jul 18 2013 nr.11.phd
-rw-r--r-- 1 jp jp 1210202 Jul 18 2013 nr.11.phi
-rw-r--r-- 1 jp jp 447289358 Jul 28 2013 nr.11.phr
-rw-r--r-- 1 jp jp 23498808 Jul 29 2013 nr.11.pin
-rw-r--r-- 1 jp jp 24203168 Jul 28 2013 nr.11.pnd
-rw-r--r-- 1 jp jp 94588 Jul 28 2013 nr.11.pni
-rw-r--r-- 1 jp jp 11749348 Jul 27 2013 nr.11.pog
-rw-r--r-- 1 jp jp 23498632 Jul 18 2013 nr.11.ppd
-rw-r--r-- 1 jp jp 91836 Jul 18 2013 nr.11.ppi
-rw-r--r-- 1 jp jp 129861277 Jul 28 2013 nr.11.psd
-rw-r--r-- 1 jp jp 2880000 Jul 28 2013 nr.11.psi
-rw-r--r-- 1 jp jp 940598459 Jul 18 2013 nr.11.psq
-rwxrwxr-x 1 jp jp 676956011 Jan 15 15:37 nr.11.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.11.tar.gz.md5
-rw-r--r-- 1 jp jp 31481333 Jul 29 2013 nr.12.phd
-rw-r--r-- 1 jp jp 709293 Jul 29 2013 nr.12.phi
-rw-r--r-- 1 jp jp 305544173 Jul 29 2013 nr.12.phr
-rw-r--r-- 1 jp jp 13912704 Jul 29 2013 nr.12.pin
-rw-r--r-- 1 jp jp 16455256 Jul 29 2013 nr.12.pnd
-rw-r--r-- 1 jp jp 64324 Jul 29 2013 nr.12.pni
-rw-r--r-- 1 jp jp 6956296 Jul 29 2013 nr.12.pog
-rw-r--r-- 1 jp jp 13912528 Jul 29 2013 nr.12.ppd
-rw-r--r-- 1 jp jp 54396 Jul 29 2013 nr.12.ppi
-rw-r--r-- 1 jp jp 78805723 Jul 29 2013 nr.12.psd
-rw-r--r-- 1 jp jp 1689714 Jul 29 2013 nr.12.psi
-rw-r--r-- 1 jp jp 601929214 Jul 29 2013 nr.12.psq
-rwxrwxr-x 1 jp jp 430259714 Jan 15 15:37 nr.12.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:36 nr.12.tar.gz.md5
-rw-rw-r-- 1 jp jp 287 Jul 3 2013 nr.pal

$ ls -l ./wd/blast/nt
total 27592328
-rw-r--r-- 1 jp jp 15606714 Jul 11 2013 nt.00.nhd
-rw-r--r-- 1 jp jp 354619 Jul 11 2013 nt.00.nhi
-rw-rw-r-- 1 jp jp 143901557 Jul 11 2013 nt.00.nhr
-rw-rw-r-- 1 jp jp 10632512 Jul 11 2013 nt.00.nin
-rw-rw-r-- 1 jp jp 7517448 Jul 11 2013 nt.00.nnd
-rw-rw-r-- 1 jp jp 29412 Jul 11 2013 nt.00.nni
-rw-r--r-- 1 jp jp 3544172 Jul 11 2013 nt.00.nog
-rw-rw-r-- 1 jp jp 33654148 Jul 11 2013 nt.00.nsd
-rw-rw-r-- 1 jp jp 781352 Jul 11 2013 nt.00.nsi
-rw-rw-r-- 1 jp jp 885548985 Jul 11 2013 nt.00.nsq
-rwxrwxr-x 1 jp jp 844096699 Jan 15 15:37 nt.00.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.00.tar.gz.md5
-rw-r--r-- 1 jp jp 11428043 Jul 11 2013 nt.01.nhd
-rw-r--r-- 1 jp jp 259982 Jul 11 2013 nt.01.nhi
-rw-rw-r-- 1 jp jp 112163028 Jul 11 2013 nt.01.nhr
-rw-rw-r-- 1 jp jp 7805012 Jul 11 2013 nt.01.nin
-rw-rw-r-- 1 jp jp 5497760 Jul 11 2013 nt.01.nnd
-rw-rw-r-- 1 jp jp 21524 Jul 11 2013 nt.01.nni
-rw-r--r-- 1 jp jp 2601672 Jul 11 2013 nt.01.nog
-rw-rw-r-- 1 jp jp 23368306 Jul 11 2013 nt.01.nsd
-rw-rw-r-- 1 jp jp 533857 Jul 11 2013 nt.01.nsi
-rw-rw-r-- 1 jp jp 916724759 Jul 11 2013 nt.01.nsq
-rwxrwxr-x 1 jp jp 872697680 Jan 15 15:37 nt.01.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.01.tar.gz.md5
-rw-r--r-- 1 jp jp 11389005 Jul 11 2013 nt.02.nhd
-rw-r--r-- 1 jp jp 259093 Jul 11 2013 nt.02.nhi
-rw-rw-r-- 1 jp jp 116020656 Jul 11 2013 nt.02.nhr
-rw-rw-r-- 1 jp jp 7778348 Jul 11 2013 nt.02.nin
-rw-rw-r-- 1 jp jp 5369408 Jul 11 2013 nt.02.nnd
-rw-rw-r-- 1 jp jp 21020 Jul 11 2013 nt.02.nni
-rw-r--r-- 1 jp jp 2592784 Jul 11 2013 nt.02.nog
-rw-rw-r-- 1 jp jp 22896943 Jul 11 2013 nt.02.nsd
-rw-rw-r-- 1 jp jp 527582 Jul 11 2013 nt.02.nsi
-rw-rw-r-- 1 jp jp 849112145 Jul 11 2013 nt.02.nsq
-rwxrwxr-x 1 jp jp 809826288 Jan 15 15:37 nt.02.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.02.tar.gz.md5
-rw-r--r-- 1 jp jp 14479973 Jul 11 2013 nt.03.nhd
-rw-r--r-- 1 jp jp 329153 Jul 11 2013 nt.03.nhi
-rw-rw-r-- 1 jp jp 141943967 Jul 11 2013 nt.03.nhr
-rw-rw-r-- 1 jp jp 9869228 Jul 11 2013 nt.03.nin
-rw-rw-r-- 1 jp jp 7062080 Jul 11 2013 nt.03.nnd
-rw-rw-r-- 1 jp jp 27636 Jul 11 2013 nt.03.nni
-rw-r--r-- 1 jp jp 3289744 Jul 11 2013 nt.03.nog
-rw-rw-r-- 1 jp jp 30230727 Jul 11 2013 nt.03.nsd
-rw-rw-r-- 1 jp jp 698187 Jul 11 2013 nt.03.nsi
-rw-rw-r-- 1 jp jp 874355668 Jul 11 2013 nt.03.nsq
-rwxrwxr-x 1 jp jp 817558860 Jan 15 15:37 nt.03.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.03.tar.gz.md5
-rw-r--r-- 1 jp jp 20908211 Jul 11 2013 nt.04.nhd
-rw-r--r-- 1 jp jp 473635 Jul 11 2013 nt.04.nhi
-rw-rw-r-- 1 jp jp 191495434 Jul 11 2013 nt.04.nhr
-rw-rw-r-- 1 jp jp 14098712 Jul 11 2013 nt.04.nin
-rw-rw-r-- 1 jp jp 9990856 Jul 11 2013 nt.04.nnd
-rw-rw-r-- 1 jp jp 39076 Jul 11 2013 nt.04.nni
-rw-r--r-- 1 jp jp 4699572 Jul 11 2013 nt.04.nog
-rw-rw-r-- 1 jp jp 44072097 Jul 11 2013 nt.04.nsd
-rw-rw-r-- 1 jp jp 999883 Jul 11 2013 nt.04.nsi
-rw-rw-r-- 1 jp jp 791883849 Jul 11 2013 nt.04.nsq
-rwxrwxr-x 1 jp jp 729666293 Jan 15 15:37 nt.04.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.04.tar.gz.md5
-rw-r--r-- 1 jp jp 23761405 Jul 11 2013 nt.05.nhd
-rw-r--r-- 1 jp jp 537249 Jul 11 2013 nt.05.nhi
-rw-rw-r-- 1 jp jp 236128656 Jul 11 2013 nt.05.nhr
-rw-rw-r-- 1 jp jp 15926300 Jul 11 2013 nt.05.nin
-rw-rw-r-- 1 jp jp 12036104 Jul 11 2013 nt.05.nnd
-rw-rw-r-- 1 jp jp 47068 Jul 11 2013 nt.05.nni
-rw-r--r-- 1 jp jp 5308768 Jul 11 2013 nt.05.nog
-rw-rw-r-- 1 jp jp 53877620 Jul 11 2013 nt.05.nsd
-rw-rw-r-- 1 jp jp 1192265 Jul 11 2013 nt.05.nsi
-rw-rw-r-- 1 jp jp 892426032 Jul 11 2013 nt.05.nsq
-rwxrwxr-x 1 jp jp 817146986 Jan 15 15:37 nt.05.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.05.tar.gz.md5
-rw-r--r-- 1 jp jp 29253684 Jul 11 2013 nt.06.nhd
-rw-r--r-- 1 jp jp 659830 Jul 11 2013 nt.06.nhi
-rw-r--r-- 1 jp jp 275044612 Jul 11 2013 nt.06.nhr
-rw-r--r-- 1 jp jp 19442960 Jul 11 2013 nt.06.nin
-rw-r--r-- 1 jp jp 14098184 Jul 11 2013 nt.06.nnd
-rw-r--r-- 1 jp jp 55116 Jul 11 2013 nt.06.nni
-rw-r--r-- 1 jp jp 6480988 Jul 11 2013 nt.06.nog
-rw-r--r-- 1 jp jp 64432449 Jul 11 2013 nt.06.nsd
-rw-r--r-- 1 jp jp 1484250 Jul 11 2013 nt.06.nsi
-rw-r--r-- 1 jp jp 891914013 Jul 11 2013 nt.06.nsq
-rwxrwxr-x 1 jp jp 787074296 Jan 15 15:37 nt.06.tar.gz
-rw-r--r-- 1 jp jp 37200369 Jul 11 2013 nt.07.nhd
-rw-r--r-- 1 jp jp 836913 Jul 11 2013 nt.07.nhi
-rw-r--r-- 1 jp jp 347051689 Jul 11 2013 nt.07.nhr
-rw-r--r-- 1 jp jp 24521384 Jul 11 2013 nt.07.nin
-rw-r--r-- 1 jp jp 17525800 Jul 11 2013 nt.07.nnd
-rw-r--r-- 1 jp jp 68508 Jul 11 2013 nt.07.nni
-rw-r--r-- 1 jp jp 8173796 Jul 11 2013 nt.07.nog
-rw-r--r-- 1 jp jp 79452374 Jul 11 2013 nt.07.nsd
-rw-r--r-- 1 jp jp 1831954 Jul 11 2013 nt.07.nsi
-rw-r--r-- 1 jp jp 811534132 Jul 11 2013 nt.07.nsq
-rwxrwxr-x 1 jp jp 687764742 Jan 15 15:37 nt.07.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.07.tar.gz.md5
-rw-r--r-- 1 jp jp 32304699 Jul 11 2013 nt.08.nhd
-rw-r--r-- 1 jp jp 727623 Jul 11 2013 nt.08.nhi
-rw-r--r-- 1 jp jp 314653209 Jul 11 2013 nt.08.nhr
-rw-r--r-- 1 jp jp 21397112 Jul 11 2013 nt.08.nin
-rw-r--r-- 1 jp jp 15835048 Jul 11 2013 nt.08.nnd
-rw-r--r-- 1 jp jp 61900 Jul 11 2013 nt.08.nni
-rw-r--r-- 1 jp jp 7132372 Jul 11 2013 nt.08.nog
-rw-r--r-- 1 jp jp 71879171 Jul 11 2013 nt.08.nsd
-rw-r--r-- 1 jp jp 1634300 Jul 11 2013 nt.08.nsi
-rw-r--r-- 1 jp jp 789666815 Jul 11 2013 nt.08.nsq
-rwxrwxr-x 1 jp jp 658761225 Jan 15 15:37 nt.08.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.08.tar.gz.md5
-rw-r--r-- 1 jp jp 25416090 Jul 11 2013 nt.09.nhd
-rw-r--r-- 1 jp jp 574014 Jul 11 2013 nt.09.nhi
-rw-r--r-- 1 jp jp 253452885 Jul 11 2013 nt.09.nhr
-rw-r--r-- 1 jp jp 16985204 Jul 11 2013 nt.09.nin
-rw-r--r-- 1 jp jp 12605072 Jul 11 2013 nt.09.nnd
-rw-r--r-- 1 jp jp 49284 Jul 11 2013 nt.09.nni
-rw-r--r-- 1 jp jp 5661736 Jul 11 2013 nt.09.nog
-rw-r--r-- 1 jp jp 55619572 Jul 11 2013 nt.09.nsd
-rw-r--r-- 1 jp jp 1240024 Jul 11 2013 nt.09.nsi
-rw-r--r-- 1 jp jp 689914284 Jul 11 2013 nt.09.nsq
-rwxrwxr-x 1 jp jp 573158597 Jan 15 15:37 nt.09.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.09.tar.gz.md5
-rw-r--r-- 1 jp jp 23418907 Jul 4 2013 nt.10.nhd
-rw-r--r-- 1 jp jp 529451 Jul 4 2013 nt.10.nhi
-rw-r--r-- 1 jp jp 234575312 Jul 11 2013 nt.10.nhr
-rw-r--r-- 1 jp jp 15707024 Jul 11 2013 nt.10.nin
-rw-r--r-- 1 jp jp 11664368 Jul 11 2013 nt.10.nnd
-rw-r--r-- 1 jp jp 45612 Jul 11 2013 nt.10.nni
-rw-r--r-- 1 jp jp 5235676 Jul 11 2013 nt.10.nog
-rw-r--r-- 1 jp jp 52191505 Jul 11 2013 nt.10.nsd
-rw-r--r-- 1 jp jp 1221931 Jul 11 2013 nt.10.nsi
-rw-r--r-- 1 jp jp 933780846 Jul 4 2013 nt.10.nsq
-rwxrwxr-x 1 jp jp 814801293 Jan 15 15:37 nt.10.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.10.tar.gz.md5
-rw-r--r-- 1 jp jp 37150699 Jul 11 2013 nt.11.nhd
-rw-r--r-- 1 jp jp 835767 Jul 11 2013 nt.11.nhi
-rw-r--r-- 1 jp jp 377177380 Jul 11 2013 nt.11.nhr
-rw-r--r-- 1 jp jp 24497780 Jul 11 2013 nt.11.nin
-rw-r--r-- 1 jp jp 17965392 Jul 11 2013 nt.11.nnd
-rw-r--r-- 1 jp jp 70228 Jul 11 2013 nt.11.nni
-rw-r--r-- 1 jp jp 8165928 Jul 11 2013 nt.11.nog
-rw-r--r-- 1 jp jp 81080774 Jul 11 2013 nt.11.nsd
-rw-r--r-- 1 jp jp 1787869 Jul 11 2013 nt.11.nsi
-rw-r--r-- 1 jp jp 968527754 Jul 11 2013 nt.11.nsq
-rwxrwxr-x 1 jp jp 800211816 Jan 15 15:37 nt.11.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.11.tar.gz.md5
-rw-r--r-- 1 jp jp 44999012 Jul 11 2013 nt.12.nhd
-rw-r--r-- 1 jp jp 1010583 Jul 11 2013 nt.12.nhi
-rw-r--r-- 1 jp jp 402368194 Jul 11 2013 nt.12.nhr
-rw-r--r-- 1 jp jp 29524604 Jul 11 2013 nt.12.nin
-rw-r--r-- 1 jp jp 20600008 Jul 11 2013 nt.12.nnd
-rw-r--r-- 1 jp jp 80516 Jul 11 2013 nt.12.nni
-rw-r--r-- 1 jp jp 9841536 Jul 11 2013 nt.12.nog
-rw-r--r-- 1 jp jp 102513123 Jul 11 2013 nt.12.nsd
-rw-r--r-- 1 jp jp 2206664 Jul 11 2013 nt.12.nsi
-rw-r--r-- 1 jp jp 989917318 Jul 11 2013 nt.12.nsq
-rwxrwxr-x 1 jp jp 888414797 Jan 15 15:37 nt.12.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.12.tar.gz.md5
-rwxrwxr-x 1 jp jp 1191426722 Jan 15 15:37 nt.13.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.13.tar.gz.md5
-rwxrwxr-x 1 jp jp 949661706 Jan 15 15:37 nt.14.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.14.tar.gz.md5
-rwxrwxr-x 1 jp jp 65174200 Jan 15 15:37 nt.15.tar.gz
-rwxrwxr-x 1 jp jp 47 Jan 15 15:37 nt.15.tar.gz.md5
-rw-rw-r-- 1 jp jp 217 Jul 6 2013 nt.nal

I am sorry for letting you know that I am using tophat-fusion-post using following commands:
$ PATH=$PATH:./wd/ncbi-blast-2.2.29+/bin
$ PATH=$PATH:./wd/blast
$ PATH=$PATH:./wd/blast/nr
$ PATH=$PATH:./wd/blast/nt
$ PATH=$PATH:./wd/blast
$ tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /path/to/h_sapiens/bowtie_index
Errors:
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [./wd/blast/nr]
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [./wd/blast/nt]
??????????????????????????
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Old 03-19-2014, 05:34 PM   #20
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
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Is your directory structure in the format that "tophat-fusion-post" requires as noted here: http://tophat.cbcb.umd.edu/fusion_tu...html#directory

Looks like you have to put all the database index files (human_genomic*, other_genomic*, and nt*) in a directory called "blast" under the (top_dir).
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