search

dariogf / SeqtrimNext

SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data. It makes use of scbi_mapreduce gem to be able to run in parallel and distributed environments. It is specially suited for Roche 454 (normal and paired-end) & Ilumina datasets, although it could be easyly adapted to any other situation.
http://www.scbi.uma.es/downloads
MIT License
2 stars 0 forks source link

wrong adapter file in Illumina templates #4

Closed visoca closed 7 years ago

visoca commented 7 years ago

There is something wrong with the default Illumina template files (genomics_short_reads.txt, genomics_short_reads_2.txt, transcriptomics_short_reads.txt). Using them throw the following error:

I, [2016-12-01 17:10:13#21763] INFO -- : SeqTrimNext version 2.0.66 I, [2016-12-01 17:10:13#21763] INFO -- : STN command: /usr/local/ruby/current/bin/seqtrimnext I, [2016-12-01 17:10:13#21763] INFO -- : Using BLASTDB: /usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/DB/formatted I, [2016-12-01 17:10:13#21763] INFO -- : Using options: {"server_ip":"0.0.0.0","port":0,"workers":6,"only_workers":false,"check_db":false,"use_checkpoint":false,"install_db":null,"logfile":"#","fastq":["./seq_1.fq.gz","./seq2.fq.gz"],"format":null,"fasta":null,"qual":null,"list_db":null,"list_db_name":"ALL","gen_params":false,"template":"./transcriptomics_short_reads.txt","chunk_size":5000,"json":null,"skip_output":false,"skip_report":false,"write_in_gzip":false} I, [2016-12-01 17:10:13#21763] INFO -- : Using init file: /usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/init_env I, [2016-12-01 17:10:13#21763] INFO -- : Using params file: transcriptomics_short_reads.txt I, [2016-12-01 17:10:13#21763] INFO -- : Used FastQ format for input files: sanger I, [2016-12-01 17:10:13#21763] INFO -- : Loading params D, [2016-12-01 17:10:13#21763] DEBUG -- : read: plugin_list =PluginIndeterminations,PluginFindPolyAt,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity D, [2016-12-01 17:10:13#21763] DEBUG -- : read: contaminants_db="contaminants.fasta cont_ribosome.fasta" D, [2016-12-01 17:10:13#21763] DEBUG -- : read: generate_initial_stats =false D, [2016-12-01 17:10:13#21763] DEBUG -- : read: min_insert_size_trimmed =30 D, [2016-12-01 17:10:13#21763] DEBUG -- : read: remove_clonality=false D, [2016-12-01 17:10:13#21763] DEBUG -- : read: adapters_ab_db="adapters_illumina.fasta" I, [2016-12-01 17:10:13#21763] INFO -- : Checking global params I, [2016-12-01 17:10:13#21763] INFO -- : Loading actions I, [2016-12-01 17:10:14#21763] INFO -- : Loading plugins [PluginIndeterminations,PluginFindPolyAt,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity,PluginExtractInserts] I, [2016-12-01 17:10:14#21763] INFO -- : Check plugin params DB file /usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/DB/formatted/adapters_illumina.fasta not formatted E, [2016-12-01 17:10:14#21763] ERROR -- : PluginAbAdapters found following errors: E, [2016-12-01 17:10:14#21763] ERROR -- : -Param adapters_ab_db is not a valid DB. Current value is #"adapters_illumina.fasta"#. Can't format database. We don't have write permissions in: /usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/DB/formatted/adapters_illumina.fasta USED DATABASES "/usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/DB/formatted/cont_ribosome.fasta /usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/DB/formatted/contaminants.fasta" USED DATABASES "/usr/local/ruby/2.0.0/lib/ruby/gems/2.0.0/gems/seqtrimnext-2.0.66/lib/seqtrimnext/DB/formatted/vectors.fasta" E, [2016-12-01 17:10:14#21763] ERROR -- : Plugin check failed

I am not sure if this fix is appropriate, but I have overcome this by including adapters_illumina DB in lib/seqtrimnext/classes/install_database.rb:

  1 require 'open-uri'
  2 
  3 class InstallDatabase
  4 
  5 
  6   def initialize(type,db_path)
  7 
  8
  9     types=['core', **'adapters_illumina',** 'cont_bacteria','cont_fungi','cont_mitochondrias','cont_plastids','cont_ribosome','cont_viruses']

followed by installation and formatting:

seqtrimnext -i adapters_illumina
seqtrimnext -c
dariogf commented 7 years ago

Thanks visoca, the solution that you have pathched yourself is the only one. I will fix STN trunk for next release.