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wurmlab / sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
https://sequenceserver.com
GNU Affero General Public License v3.0
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scan_blast_db error on startup #50

Closed prohan closed 13 years ago

prohan commented 13 years ago

Hi I'm trying to run sequenceserver on Ubuntu 11.04 with Ruby 1.8.7.

I get the following when trying to start:

== Initializing SequenceServer... I, [2011-09-08T18:14:33.420921 #32651] INFO -- : Found blastx at /usr/local/bin/blastx I, [2011-09-08T18:14:33.421086 #32651] INFO -- : Found blastn at /usr/local/bin/blastn I, [2011-09-08T18:14:33.421177 #32651] INFO -- : Found blastdbcmd at /usr/local/bin/blastdbcmd I, [2011-09-08T18:14:33.421258 #32651] INFO -- : Found blastp at /usr/local/bin/blastp I, [2011-09-08T18:14:33.421339 #32651] INFO -- : Found tblastx at /usr/local/bin/tblastx I, [2011-09-08T18:14:33.421419 #32651] INFO -- : Found makeblastdb at /usr/local/bin/makeblastdb I, [2011-09-08T18:14:33.421502 #32651] INFO -- : Found tblastn at /usr/local/bin/tblastn ./lib/helpers.rb:94:in scan_blast_db': undefined methoddowncase' for nil:NilClass (NoMethodError) from ./lib/helpers.rb:92:in each_line' from ./lib/helpers.rb:92:inscan_blast_db' from sequenceserver.rb:168:in init' from sequenceserver.rb:113:inrun!' from sequenceserver.rb:383 from sequenceserver.rb:383

yannickwurm commented 13 years ago

Hi there,

thanks for the bug report. Looks like blastdbcmd either isn't working or is returning an empty line (which I haven't seen before).

2 questions:

  1. which version of blast are you using?
  2. is blastdbcmd in your $PATH? (if not, please try adding it).

cheers, yannick

On 9 Sep 2011, at 09:17, prohan wrote:

Hi I'm trying to run sequenceserver on Ubuntu 11.04 with Ruby 1.8.7.

I get the following when trying to start:

== Initializing SequenceServer... I, [2011-09-08T18:14:33.420921 #32651] INFO -- : Found blastx at /usr/local/bin/blastx I, [2011-09-08T18:14:33.421086 #32651] INFO -- : Found blastn at /usr/local/bin/blastn I, [2011-09-08T18:14:33.421177 #32651] INFO -- : Found blastdbcmd at /usr/local/bin/blastdbcmd I, [2011-09-08T18:14:33.421258 #32651] INFO -- : Found blastp at /usr/local/bin/blastp I, [2011-09-08T18:14:33.421339 #32651] INFO -- : Found tblastx at /usr/local/bin/tblastx I, [2011-09-08T18:14:33.421419 #32651] INFO -- : Found makeblastdb at /usr/local/bin/makeblastdb I, [2011-09-08T18:14:33.421502 #32651] INFO -- : Found tblastn at /usr/local/bin/tblastn ./lib/helpers.rb:94:in scan_blast_db': undefined methoddowncase' for nil:NilClass (NoMethodError) from ./lib/helpers.rb:92:in each_line' from ./lib/helpers.rb:92:inscan_blast_db' from sequenceserver.rb:168:in init' from sequenceserver.rb:113:inrun!' from sequenceserver.rb:383 from sequenceserver.rb:383

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50

prohan commented 13 years ago

BLAST 2.2.22+ and blastdbcmd is in my path.

Thanks for the quicky reply.

Rohan

On Thu, Sep 8, 2011 at 6:40 PM, Yannick Wurm reply@reply.github.com wrote:

Hi there,

thanks for the bug report. Looks like blastdbcmd either isn't working or is returning an empty line (which I haven't seen before).

2 questions:   1. which version of blast are you using?   2. is blastdbcmd in your $PATH?   (if not, please try adding it).

cheers, yannick

On 9 Sep 2011, at 09:17, prohan wrote:

Hi I'm trying to run sequenceserver on Ubuntu 11.04 with Ruby 1.8.7.

I get the following when trying to start:

== Initializing SequenceServer... I, [2011-09-08T18:14:33.420921 #32651]  INFO -- : Found blastx at /usr/local/bin/blastx I, [2011-09-08T18:14:33.421086 #32651]  INFO -- : Found blastn at /usr/local/bin/blastn I, [2011-09-08T18:14:33.421177 #32651]  INFO -- : Found blastdbcmd at /usr/local/bin/blastdbcmd I, [2011-09-08T18:14:33.421258 #32651]  INFO -- : Found blastp at /usr/local/bin/blastp I, [2011-09-08T18:14:33.421339 #32651]  INFO -- : Found tblastx at /usr/local/bin/tblastx I, [2011-09-08T18:14:33.421419 #32651]  INFO -- : Found makeblastdb at /usr/local/bin/makeblastdb I, [2011-09-08T18:14:33.421502 #32651]  INFO -- : Found tblastn at /usr/local/bin/tblastn ./lib/helpers.rb:94:in scan_blast_db': undefined methoddowncase' for nil:NilClass (NoMethodError)       from ./lib/helpers.rb:92:in each_line'       from ./lib/helpers.rb:92:inscan_blast_db'       from sequenceserver.rb:168:in init'       from sequenceserver.rb:113:inrun!'       from sequenceserver.rb:383       from sequenceserver.rb:383

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50#issuecomment-2047161

yannickwurm commented 13 years ago

could you perhaps try a newer version of blast?

I have the feeling blastdbcmd's output may have changed without noticing.

y

On 9 Sep 2011, at 09:52, prohan wrote:

BLAST 2.2.22+ and blastdbcmd is in my path.

Thanks for the quicky reply.

Rohan

On Thu, Sep 8, 2011 at 6:40 PM, Yannick Wurm reply@reply.github.com wrote:

Hi there,

thanks for the bug report. Looks like blastdbcmd either isn't working or is returning an empty line (which I haven't seen before).

2 questions:

  1. which version of blast are you using?
  2. is blastdbcmd in your $PATH? (if not, please try adding it).

cheers, yannick

On 9 Sep 2011, at 09:17, prohan wrote:

Hi I'm trying to run sequenceserver on Ubuntu 11.04 with Ruby 1.8.7.

I get the following when trying to start:

== Initializing SequenceServer... I, [2011-09-08T18:14:33.420921 #32651] INFO -- : Found blastx at /usr/local/bin/blastx I, [2011-09-08T18:14:33.421086 #32651] INFO -- : Found blastn at /usr/local/bin/blastn I, [2011-09-08T18:14:33.421177 #32651] INFO -- : Found blastdbcmd at /usr/local/bin/blastdbcmd I, [2011-09-08T18:14:33.421258 #32651] INFO -- : Found blastp at /usr/local/bin/blastp I, [2011-09-08T18:14:33.421339 #32651] INFO -- : Found tblastx at /usr/local/bin/tblastx I, [2011-09-08T18:14:33.421419 #32651] INFO -- : Found makeblastdb at /usr/local/bin/makeblastdb I, [2011-09-08T18:14:33.421502 #32651] INFO -- : Found tblastn at /usr/local/bin/tblastn ./lib/helpers.rb:94:in scan_blast_db': undefined methoddowncase' for nil:NilClass (NoMethodError) from ./lib/helpers.rb:92:in each_line' from ./lib/helpers.rb:92:inscan_blast_db' from sequenceserver.rb:168:in init' from sequenceserver.rb:113:inrun!' from sequenceserver.rb:383 from sequenceserver.rb:383

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50#issuecomment-2047161

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50#issuecomment-2047222

prohan commented 13 years ago

Looks like that it fixed it. I'm on BLAST 2.2.25+ now.

That's what's in the bio-linux repo.

Thanks!

On Thu, Sep 8, 2011 at 7:02 PM, Yannick Wurm reply@reply.github.com wrote:

could you perhaps try a newer version of blast?

I have the feeling blastdbcmd's output may have changed without noticing.

 * perhaps it formats completely differently... in which case you need to try puttng a newer version of blast in your path.  (avoid 2.2.24 because parse_seqids is broken in that one)  * or perhaps it adds a blank line... in this case, try inserting next if type.nil? on a new line between line 93 and 94 of lib/helpers.rb

y

On 9 Sep 2011, at 09:52, prohan wrote:

BLAST 2.2.22+ and blastdbcmd is in my path.

Thanks for the quicky reply.

Rohan

On Thu, Sep 8, 2011 at 6:40 PM, Yannick Wurm reply@reply.github.com wrote:

Hi there,

thanks for the bug report. Looks like blastdbcmd either isn't working or is returning an empty line (which I haven't seen before).

2 questions:   1. which version of blast are you using?   2. is blastdbcmd in your $PATH?   (if not, please try adding it).

cheers, yannick

On 9 Sep 2011, at 09:17, prohan wrote:

Hi I'm trying to run sequenceserver on Ubuntu 11.04 with Ruby 1.8.7.

I get the following when trying to start:

== Initializing SequenceServer... I, [2011-09-08T18:14:33.420921 #32651]  INFO -- : Found blastx at /usr/local/bin/blastx I, [2011-09-08T18:14:33.421086 #32651]  INFO -- : Found blastn at /usr/local/bin/blastn I, [2011-09-08T18:14:33.421177 #32651]  INFO -- : Found blastdbcmd at /usr/local/bin/blastdbcmd I, [2011-09-08T18:14:33.421258 #32651]  INFO -- : Found blastp at /usr/local/bin/blastp I, [2011-09-08T18:14:33.421339 #32651]  INFO -- : Found tblastx at /usr/local/bin/tblastx I, [2011-09-08T18:14:33.421419 #32651]  INFO -- : Found makeblastdb at /usr/local/bin/makeblastdb I, [2011-09-08T18:14:33.421502 #32651]  INFO -- : Found tblastn at /usr/local/bin/tblastn ./lib/helpers.rb:94:in scan_blast_db': undefined methoddowncase' for nil:NilClass (NoMethodError)       from ./lib/helpers.rb:92:in each_line'       from ./lib/helpers.rb:92:inscan_blast_db'       from sequenceserver.rb:168:in init'       from sequenceserver.rb:113:inrun!'       from sequenceserver.rb:383       from sequenceserver.rb:383

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50#issuecomment-2047161

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50#issuecomment-2047222

Reply to this email directly or view it on GitHub: https://github.com/yannickwurm/sequenceserver/issues/50#issuecomment-2047278

yannickwurm commented 13 years ago

Excellent.

We should probably only "officially" support a single version of BLAST, because we don't have integration tests running on all combinations of all versions of everything.

yannickwurm commented 13 years ago

Blank lines are now skipped in

https://github.com/yannickwurm/sequenceserver/commit/ecb171a41dace08850b6448f7f5e63660dfa4d36