plugin_contaminants.rb in seqtrimnext-2.0.46

- old
+ new

@@ -34,11 +34,11 @@
     # TODO - Culling limit = 2 porque el blast falla con este comando cuando se le pasa cl=1 y dust=no
     # y una secuencia de baja complejidad como entrada
 
     blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
 
-    $LOG.info('BLAST:'+blast.get_blast_cmd(:xml))
+    $LOG.debug('BLAST:'+blast.get_blast_cmd(:xml))
 
     fastas=[]
 
     seqs.each do |seq|
       fastas.push ">"+seq.seq_name
@@ -65,11 +65,11 @@
   def exec_seq(seq,blast_query)
     if blast_query.query_id != seq.seq_name
       # raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
     end
 
-    $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for contaminants into the sequence"
+    $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for contaminants into the sequence"
 
 
     #blast = BatchBlast.new('-db DB/formatted/contaminants.fasta','blastn',' -task blastn -evalue 1e-10 -perc_identity 95')  #get contaminants
     # blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
 
@@ -141,10 +141,10 @@
             add_stats('contaminants_ids',c)
           end
 
         end
       else
-        $LOG.info('Contaminant ignored due to genus match: '+c.definition)
+        $LOG.debug('Contaminant ignored due to genus match: '+c.definition)
       end
     end
 
     reject=@params.get_param('contaminants_reject')
     # cond_if=false