Reporting bug -- cannot use the program now

Eduardo_Fox · March 24, 2015, 11:49am

Hello

I have been testing sequence server on my computer since several days. Now the program won’t launch anymore, as I get the following:

$ sequenceserver
Something went wonky

Looks like you have encountered a bug in SequenceServer. Please could you
report this incident to our Google Group -
https://groups.google.com/forum/?fromgroups#!forum/sequenceserver

Error:
undefined method downcase!' for nil:NilClass /Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver/database.rb:25:in initialize’
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver/database.rb:109:in new' /Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver/database.rb:109:in scan_databases_dir’
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver/database.rb:106:in each_line' /Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver/database.rb:106:in scan_databases_dir’
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/open3.rb:86:in popen3' /Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver/database.rb:102:in scan_databases_dir’
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver.rb:132:in init_database' /Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/lib/sequenceserver.rb:40:in init’
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/bin/sequenceserver:131
/Library/Ruby/Gems/1.8/gems/slop-3.6.0/lib/slop.rb:260:in call' /Library/Ruby/Gems/1.8/gems/slop-3.6.0/lib/slop.rb:260:in parse!’
/Library/Ruby/Gems/1.8/gems/slop-3.6.0/lib/slop.rb:65:in parse!' /Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.1/bin/sequenceserver:12 /usr/bin/sequenceserver:19:in load’
/usr/bin/sequenceserver:19

Please let me know how I can proceed to get it back up again.

Best wishes,

Anurag_Priyam · March 25, 2015, 2:03pm

It’s because of one of the following:

Incorrect permission on one of your your database file.
Database corrupted somehow.
Database incompatible with BLAST+ 2.2.30. Until now I was under the impression that this would happen only if the dbs were created with older formatdb program. But a recent thread on this mailing list makes me doubt that there’s incompatibility in the databases created by makeblastdb 2.2.25+ and 2.2.30+ as well. I will have to look into this.

In short,

check permissions on your db files
delete and recreate the dbs (SequenceServer can do the creation part automatically: sequenceserver -m)

– Priyam

Rahul_Tevatia · April 9, 2015, 12:51am

Hi Priyam,

I tried to install on mac, however facing some similar problem. Can you please help me to fix it?
Thanks a lot!
Rahul

Could not locate BLAST+ binaries.

SequenceServer can use NCBI BLAST+ that you may have on your system already, or

download the correct package for itself. Please enter the path to NCBI BLAST+

or press Enter to download.

Press Ctrl+C to quit.

Installing NCBI BLAST+.

RUBY_PLATFORM universal.x86_64-darwin14

** Resuming transfer from byte position 254664407

% Total % Received % Xferd Average Speed Time Time Time Current

Dload Upload Total Spent Left Speed

0 242M 0 0 0 0 0 0 --:–:-- 0:00:01 --:–:-- 0

x ncbi-blast-2.2.30+/

x ncbi-blast-2.2.30+/LICENSE

x ncbi-blast-2.2.30+/ChangeLog

x ncbi-blast-2.2.30+/ncbi_package_info

x ncbi-blast-2.2.30+/doc/

x ncbi-blast-2.2.30+/doc/README.txt

x ncbi-blast-2.2.30+/README

x ncbi-blast-2.2.30+/bin/

x ncbi-blast-2.2.30+/bin/tblastn

x ncbi-blast-2.2.30+/bin/blastdbcheck

x ncbi-blast-2.2.30+/bin/blast_formatter

x ncbi-blast-2.2.30+/bin/deltablast

x ncbi-blast-2.2.30+/bin/tblastx

x ncbi-blast-2.2.30+/bin/blastp

x ncbi-blast-2.2.30+/bin/makeblastdb

x ncbi-blast-2.2.30+/bin/blastn

x ncbi-blast-2.2.30+/bin/windowmasker

x ncbi-blast-2.2.30+/bin/blastdbcmd

x ncbi-blast-2.2.30+/bin/makembindex

x ncbi-blast-2.2.30+/bin/makeprofiledb

x ncbi-blast-2.2.30+/bin/update_blastdb.pl

x ncbi-blast-2.2.30+/bin/blastdb_aliastool

x ncbi-blast-2.2.30+/bin/dustmasker

x ncbi-blast-2.2.30+/bin/psiblast

x ncbi-blast-2.2.30+/bin/rpsblast

x ncbi-blast-2.2.30+/bin/rpstblastn

x ncbi-blast-2.2.30+/bin/convert2blastmask

x ncbi-blast-2.2.30+/bin/blastx

x ncbi-blast-2.2.30+/bin/segmasker

x ncbi-blast-2.2.30+/bin/legacy_blast.pl

Database dir not set.

SequenceServer needs to know where your FASTA files or BLAST+ databases are.

Please enter the path to the relevant directory (default: current directory).

Press Ctrl+C to quit.

/Users/Rahul/Desktop/395-Sequences

Something went wonky

Looks like you have encountered a bug in SequenceServer. Please could you

report this incident to our Google Group -

https://groups.google.com/forum/?fromgroups#!forum/sequenceserver

Error:

undefined method `downcase!’ for nil:NilClass

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:25:in `initialize’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:109:in `new’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:109:in `block (2 levels) in scan_databases_dir’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:106:in `each_line’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:106:in `block in scan_databases_dir’

/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/open3.rb:217:in `popen_run’

/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/open3.rb:99:in `popen3’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:102:in `scan_databases_dir’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver.rb:130:in `init_database’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver.rb:40:in `init’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/bin/sequenceserver:131:in `block (2 levels) in <top (required)>’

/Library/Ruby/Gems/2.0.0/gems/slop-3.6.0/lib/slop.rb:260:in `call’

/Library/Ruby/Gems/2.0.0/gems/slop-3.6.0/lib/slop.rb:260:in `parse!’

/Library/Ruby/Gems/2.0.0/gems/slop-3.6.0/lib/slop.rb:65:in `parse!’

/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/bin/sequenceserver:12:in `<top (required)>’

/usr/bin/sequenceserver:23:in `load’

/usr/bin/sequenceserver:23:in `’

Anurag_Priyam · April 16, 2015, 12:26pm

Hey Rahul,

Sorry about the slow response. Have you been able to work around this issue already? If not, I suggest you delete all blast databases from /Users/Rahul/Desktop/395-Sequences (assuming there aren’t 395 of them). BLAST databases end in .nhr, .nin, etc. extension. Then run SequenceServer. It will complain there are no BLAST database in that directory and ask you if you want to create them now. It will scan the directory (and subdirectories) for all FASTA files and prompt you for yes/no.

I hope this helps.

– Priyam