Parameters File Error
Closed this issue · 3 comments
I am trying to use the checkbaits pipeline the pipeline works fine until I use the -w or parameters flag when I get the following error, What would be the best way to rectify this to get my params file, thank you!
Starting program with the following options: **
** Basic command: checkbaits -i CP_FixedOffset_ProteinCoding_Baits.txt -L120 -o CP_FixedOffset_ProteinCoding_Baits -Z /Users/mkandat/Desktop/RNAseq_Baits/Final_Baits_Strategy -G include -X1 --rng 157955052007280791904245408599035640797 **
** Filtration options: -w **
** Using BaitsTools v. 1.7.5, checkbaits v. 1.7.0, and baitslib v. 1.7.5 **
** Reading FASTA/FASTQ **
** Filtering 120 baits **
#<Thread:0x000000010972e2a0 /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:17 run> terminated with exception (report_on_exception is true):
/Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:329:in block (3 levels) in max_homopolymer': undefined method include?' for nil:NilClass (NoMethodError)
posbases.delete(posbase) unless nextposbases.include?(posbase)
^^^^^^^^^
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:328:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:328:in `block (2 levels) in max_homopolymer'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:326:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:326:in `block in max_homopolymer'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:321:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:321:in `max_homopolymer'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:392:in `filter_baits'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:28:in `block (3 levels) in multi_checkbaits'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:18:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:18:in `block (2 levels) in multi_checkbaits'
/Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:329:in block (3 levels) in max_homopolymer': undefined method include?' for nil:NilClass (NoMethodError)
posbases.delete(posbase) unless nextposbases.include?(posbase)
^^^^^^^^^
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:328:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:328:in `block (2 levels) in max_homopolymer'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:326:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:326:in `block in max_homopolymer'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:321:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:321:in `max_homopolymer'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/baitslib.rb:392:in `filter_baits'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:28:in `block (3 levels) in multi_checkbaits'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:18:in `each'
from /Users/mkandat/.rvm/rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/gems/baitstools-1.7.5/lib/checkbaits.rb:18:in `block (2 levels) in multi_checkbaits'
Could you send me your input file (campanam@si.edu)?
The most likely reason is your bait includes a character that BaitsTools does not recognize and know how to convert into a IUPAC ambiguity code.
Thank you that is good to know, I've sent over the file and will also try to remake it!