wurmlab / npsearch Goto Github PK
View Code? Open in Web Editor NEWNpSearch: Search for Neuropeptides
License: GNU Affero General Public License v3.0
npsearch's People
Contributors
Stargazers
Watchers
Forkers
yannickwurmnpsearch's Issues
Errors about "undefined method `split' for nil:NilClass (NoMethodError)"
Hello,
I installed NpSearch on 3 linux workstations, and got errors about "undefined method `split' for nil:NilClass (NoMethodError)".
They installed version 2.1.4 and 2.1.5 on ruby 2.4.0 (ubuntu 14.04)
2 of them sent error messages like below when I test NpSearch with protein.fa from test directory.
npsearch -n 40 -d protein.fa > debug.log
/var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/scoresequence.rb:81:in `np_similarity': undefined method `split' for nil:NilClass (NoMethodError)
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/scoresequence.rb:17:in `run'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch.rb:87:in `initialise_seqs'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch.rb:73:in `block (2 levels) in iterate_input_file'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/pool.rb:37:in `block (4 levels) in initialize'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/pool.rb:35:in `loop'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/pool.rb:35:in `block (3 levels) in initialize'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/pool.rb:34:in `catch'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.5/lib/npsearch/pool.rb:34:in `block (2 levels) in initialize'
and... 1 of them sent error message like this.
npsearch -n 48 /var/lib/gems/2.4.0/gems/npsearch-2.1.4/test/files/protein.fa
/var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch/sequence.rb:22:in `initialize': undefined method `[]' for nil:NilClass (NoMethodError)
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch.rb:86:in `new'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch.rb:86:in `initialise_seqs'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch.rb:73:in `block (2 levels) in iterate_input_file'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch/pool.rb:37:in `block (4 levels) in initialize'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch/pool.rb:35:in `loop'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch/pool.rb:35:in `block (3 levels) in initialize'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch/pool.rb:34:in `catch'
from /var/lib/gems/2.4.0/gems/npsearch-2.1.4/lib/npsearch/pool.rb:34:in `block (2 levels) in initialize'
and... let you show debug file.
D, [2017-01-25T23:58:22.382356 #36456] DEBUG -- : Testing if the input fasta file exists: 'protein.fa'.
D, [2017-01-25T23:58:22.382423 #36456] DEBUG -- : Testing if the input file ('/home/macarima/bioapps/npsearch/test/files/protein.fa') is empty.
D, [2017-01-25T23:58:22.382449 #36456] DEBUG -- : Testing whether the input, ('/home/macarima/bioapps/npsearch/test/files/protein.fa') is a fasta file.
D, [2017-01-25T23:58:22.382487 #36456] DEBUG -- : Checking the type of sequence in the input file based on the first 500 lines.
D, [2017-01-25T23:58:22.424464 #36456] DEBUG -- : The guessed typed of Sequences are: [:protein]
D, [2017-01-25T23:58:22.424499 #36456] DEBUG -- : Checking the number of threads: 40
D, [2017-01-25T23:58:22.424515 #36456] DEBUG -- : Checking SignalP 4.1 Script binary at: signalp.
D, [2017-01-25T23:58:22.426889 #36456] DEBUG -- : The validated OPT hash contains: {:signalp_path=>"signalp", :temp_dir=>"/home/macarima/bioapps/npsearch/test/files/.temp/20170125-36456-13j2yn2", :num_threads=>40, :debug=>true, :min_orf_length=>30, :max_orf_length=>600, :input_file=>"/home/macarima/bioapps/npsearch/test/files/protein.fa", :type=>:protein}
D, [2017-01-25T23:58:22.426921 #36456] DEBUG -- : Creating a thread pool of size 40
D, [2017-01-25T23:58:22.432482 #36456] DEBUG -- : Successfully creating temp directory at: /home/macarima/bioapps/npsearch/test/files/.temp/20170125-36456-13j2yn2
D, [2017-01-25T23:58:22.432537 #36456] DEBUG -- : Iterating the Input File: /home/macarima/bioapps/npsearch/test/files/protein.fa
D, [2017-01-25T23:58:22.466209 #36456] DEBUG -- : -- Analysing: 'isotig00001_f1' (728)
D, [2017-01-25T23:58:22.466325 #36456] DEBUG -- : -- Analysing: 'isotig00001_f2' (728)
D, [2017-01-25T23:58:22.466379 #36456] DEBUG -- : -- Analysing: 'isotig00001_f3' (727)
D, [2017-01-25T23:58:22.466426 #36456] DEBUG -- : -- Analysing: 'isotig00001_f4' (728)
D, [2017-01-25T23:58:22.466511 #36456] DEBUG -- : -- Analysing: 'isotig00001_f5' (728)
D, [2017-01-25T23:58:22.466554 #36456] DEBUG -- : -- Analysing: 'isotig00001_f6' (727)
D, [2017-01-25T23:58:22.466594 #36456] DEBUG -- : -- Analysing: 'isotig00002_f1' (638)
D, [2017-01-25T23:58:22.466632 #36456] DEBUG -- : -- Analysing: 'isotig00002_f2' (637)
D, [2017-01-25T23:58:22.466675 #36456] DEBUG -- : -- Analysing: 'isotig00002_f3' (637)
D, [2017-01-25T23:58:22.466714 #36456] DEBUG -- : -- Analysing: 'isotig00002_f4' (638)
D, [2017-01-25T23:58:22.466753 #36456] DEBUG -- : -- Analysing: 'isotig00002_f5' (637)
D, [2017-01-25T23:58:22.466794 #36456] DEBUG -- : -- Analysing: 'isotig00002_f6' (637)
D, [2017-01-25T23:58:22.466833 #36456] DEBUG -- : -- Analysing: 'isotig00003_f1' (639)
D, [2017-01-25T23:58:22.466875 #36456] DEBUG -- : -- Analysing: 'isotig00003_f2' (638)
D, [2017-01-25T23:58:22.466913 #36456] DEBUG -- : -- Analysing: 'isotig00003_f3' (638)
D, [2017-01-25T23:58:22.466955 #36456] DEBUG -- : -- Analysing: 'isotig00003_f4' (639)
D, [2017-01-25T23:58:22.466998 #36456] DEBUG -- : -- Analysing: 'isotig00003_f5' (638)
D, [2017-01-25T23:58:22.467037 #36456] DEBUG -- : -- Analysing: 'isotig00003_f6' (638)
D, [2017-01-25T23:58:22.467078 #36456] DEBUG -- : -- Analysing: 'isotig00004_f1' (632)
D, [2017-01-25T23:58:22.467116 #36456] DEBUG -- : -- Analysing: 'isotig00004_f2' (631)
D, [2017-01-25T23:58:22.467157 #36456] DEBUG -- : -- Analysing: 'isotig00004_f3' (631)
D, [2017-01-25T23:58:22.467216 #36456] DEBUG -- : -- Analysing: 'isotig00004_f4' (632)
D, [2017-01-25T23:58:22.467254 #36456] DEBUG -- : -- Analysing: 'isotig00004_f5' (631)
D, [2017-01-25T23:58:22.467299 #36456] DEBUG -- : -- Analysing: 'isotig00004_f6' (631)
D, [2017-01-25T23:58:22.467337 #36456] DEBUG -- : -- Analysing: 'isotig00005_f1' (596)
D, [2017-01-25T23:58:22.468225 #36456] DEBUG -- : -- Analysing: 'isotig00005_f2' (596)
D, [2017-01-25T23:58:22.469046 #36456] DEBUG -- : -- Analysing: 'isotig00005_f3' (595)
D, [2017-01-25T23:58:22.469902 #36456] DEBUG -- : -- Analysing: 'isotig00005_f4' (596)
D, [2017-01-25T23:58:22.471054 #36456] DEBUG -- : -- Analysing: 'isotig00005_f5' (596)
D, [2017-01-25T23:58:22.471460 #36456] DEBUG -- : -- Analysing: 'isotig00005_f6' (595)
D, [2017-01-25T23:58:22.471841 #36456] DEBUG -- : -- Analysing: 'isotig00006_f1' (582)
D, [2017-01-25T23:58:22.472240 #36456] DEBUG -- : -- Analysing: 'isotig00006_f2' (582)
D, [2017-01-25T23:58:22.472692 #36456] DEBUG -- : -- Analysing: 'isotig00006_f3' (581)
D, [2017-01-25T23:58:22.473142 #36456] DEBUG -- : -- Analysing: 'isotig00006_f4' (582)
D, [2017-01-25T23:58:22.473532 #36456] DEBUG -- : -- Analysing: 'isotig00006_f5' (582)
D, [2017-01-25T23:58:22.473856 #36456] DEBUG -- : -- Analysing: 'isotig00006_f6' (581)
D, [2017-01-25T23:58:22.474214 #36456] DEBUG -- : -- Analysing: 'isotig00007_f1' (583)
D, [2017-01-25T23:58:22.475931 #36456] DEBUG -- : -- Analysing: 'isotig00007_f2' (582)
D, [2017-01-25T23:58:22.476318 #36456] DEBUG -- : -- Analysing: 'isotig00007_f3' (582)
D, [2017-01-25T23:58:22.476752 #36456] DEBUG -- : -- Analysing: 'isotig00007_f4' (583)
D, [2017-01-25T23:58:22.477174 #36456] DEBUG -- : -- Analysing: 'isotig00007_f5' (582)
D, [2017-01-25T23:58:22.477546 #36456] DEBUG -- : -- Analysing: 'isotig00007_f6' (582)
D, [2017-01-25T23:58:22.477936 #36456] DEBUG -- : -- Analysing: 'isotig00008_f1' (575)
D, [2017-01-25T23:58:22.478290 #36456] DEBUG -- : -- Analysing: 'isotig00008_f2' (575)
D, [2017-01-25T23:58:22.478687 #36456] DEBUG -- : -- Analysing: 'isotig00008_f3' (574)
D, [2017-01-25T23:58:22.479812 #36456] DEBUG -- : -- Analysing: 'isotig00008_f4' (575)
D, [2017-01-25T23:58:22.480164 #36456] DEBUG -- : -- Analysing: 'isotig00008_f5' (575)
D, [2017-01-25T23:58:22.480627 #36456] DEBUG -- : -- Analysing: 'isotig00008_f6' (574)
D, [2017-01-25T23:58:22.481044 #36456] DEBUG -- : -- Analysing: 'isotig00009_f1' (609)
D, [2017-01-25T23:58:22.481130 #36456] DEBUG -- : -- Analysing: 'isotig00009_f2' (608)
D, [2017-01-25T23:58:22.481204 #36456] DEBUG -- : -- Analysing: 'isotig00009_f3' (608)
D, [2017-01-25T23:58:22.481262 #36456] DEBUG -- : -- Analysing: 'isotig00009_f4' (609)
D, [2017-01-25T23:58:22.481308 #36456] DEBUG -- : -- Analysing: 'isotig00009_f5' (608)
D, [2017-01-25T23:58:22.481350 #36456] DEBUG -- : -- Analysing: 'isotig00009_f6' (608)
D, [2017-01-25T23:58:22.481396 #36456] DEBUG -- : -- Analysing: 'isotig00010_f1' (550)
D, [2017-01-25T23:58:22.481753 #36456] DEBUG -- : -- Analysing: 'isotig00010_f2' (549)
D, [2017-01-25T23:58:22.484191 #36456] DEBUG -- : -- Analysing: 'isotig00010_f3' (549)
D, [2017-01-25T23:58:22.484589 #36456] DEBUG -- : -- Analysing: 'isotig00010_f4' (550)
D, [2017-01-25T23:58:22.484896 #36456] DEBUG -- : -- Analysing: 'isotig00010_f5' (549)
D, [2017-01-25T23:58:22.485227 #36456] DEBUG -- : -- Analysing: 'isotig00010_f6' (549)
D, [2017-01-25T23:58:22.485597 #36456] DEBUG -- : -- Analysing: 'isotig00011_f1' (508)
D, [2017-01-25T23:58:22.485976 #36456] DEBUG -- : -- Analysing: 'isotig00011_f2' (508)
D, [2017-01-25T23:58:22.486399 #36456] DEBUG -- : -- Analysing: 'isotig00011_f3' (507)
D, [2017-01-25T23:58:22.486883 #36456] DEBUG -- : -- Analysing: 'isotig00011_f4' (508)
D, [2017-01-25T23:58:22.487421 #36456] DEBUG -- : -- Analysing: 'isotig00011_f5' (508)
D, [2017-01-25T23:58:22.509613 #36456] DEBUG -- : -- Analysing: 'isotig00011_f6' (507)
D, [2017-01-25T23:58:22.510061 #36456] DEBUG -- : -- Analysing: 'isotig00012_f1' (494)
D, [2017-01-25T23:58:22.510448 #36456] DEBUG -- : -- Analysing: 'isotig00012_f2' (494)
D, [2017-01-25T23:58:22.511015 #36456] DEBUG -- : -- Analysing: 'isotig00012_f3' (493)
D, [2017-01-25T23:58:22.511459 #36456] DEBUG -- : -- Analysing: 'isotig00012_f4' (494)
D, [2017-01-25T23:58:23.045235 #36456] DEBUG -- : -- Analysing: 'isotig00012_f5' (494)
D, [2017-01-25T23:58:23.143812 #36456] DEBUG -- : -- Analysing: 'isotig00012_f6' (493)
D, [2017-01-25T23:58:23.199483 #36456] DEBUG -- : -- Analysing: 'isotig00013_f1' (495)
D, [2017-01-25T23:58:23.278123 #36456] DEBUG -- : -- Analysing: 'isotig00013_f2' (494)
D, [2017-01-25T23:58:23.279007 #36456] DEBUG -- : -- Analysing: 'isotig00013_f3' (494)
D, [2017-01-25T23:58:23.279429 #36456] DEBUG -- : -- Analysing: 'isotig00013_f4' (495)
D, [2017-01-25T23:58:23.287377 #36456] DEBUG -- : -- Analysing: 'isotig00013_f5' (494)
D, [2017-01-25T23:58:23.299540 #36456] DEBUG -- : -- Analysing: 'isotig00013_f6' (494)
D, [2017-01-25T23:58:23.301906 #36456] DEBUG -- : -- Analysing: 'isotig00014_f1' (486)
D, [2017-01-25T23:58:23.302219 #36456] DEBUG -- : -- Analysing: 'isotig00014_f2' (486)
D, [2017-01-25T23:58:23.302388 #36456] DEBUG -- : -- Analysing: 'isotig00014_f3' (485)
D, [2017-01-25T23:58:23.303625 #36456] DEBUG -- : -- Analysing: 'isotig00014_f4' (486)
D, [2017-01-25T23:58:23.309871 #36456] DEBUG -- : -- Analysing: 'isotig00014_f5' (486)
D, [2017-01-25T23:58:23.312765 #36456] DEBUG -- : -- Analysing: 'isotig00014_f6' (485)
D, [2017-01-25T23:58:23.321314 #36456] DEBUG -- : -- Analysing: 'isotig00015_f1' (379)
D, [2017-01-25T23:58:23.323473 #36456] DEBUG -- : -- Analysing: 'isotig00015_f2' (379)
D, [2017-01-25T23:58:23.328402 #36456] DEBUG -- : -- Analysing: 'isotig00015_f3' (378)
D, [2017-01-25T23:58:23.329827 #36456] DEBUG -- : -- Analysing: 'isotig00015_f4' (379)
D, [2017-01-25T23:58:23.348442 #36456] DEBUG -- : -- Analysing: 'isotig00015_f5' (379)
D, [2017-01-25T23:58:23.363302 #36456] DEBUG -- : -- Analysing: 'isotig00015_f6' (378)
What's wrong about this situation?
Thank you for your help.
Best,
Hui-Su Kim.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.