Commit 13dbbc4f authored by Penom Nom's avatar Penom Nom
Browse files

redirect stderr to stderr file for uchime chimera

parent ec8ddd48
......@@ -51,21 +51,22 @@ class MothurChimeraUchime(Component):
self.uchime_chimera_files = OutputFileList(self.get_outputs('{basename_woext}.uchime.chimeras', self.fasta_files), Formats.FASTA)
self.uchime_accnos_files = OutputFileList(self.get_outputs('{basename_woext}.uchime.accnos', self.fasta_files), Formats.MOTHUR_ACCNOS)
self.stdout = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.fasta_files))
self.stderr = OutputFileList(self.get_outputs('{basename_woext}.stderr', self.fasta_files))
def process(self):
if self.reference_files:
chimerauchime = ShellFunction(self.get_exec_path("mothur") + ' "#chimera.uchime(fasta=$1,reference=$2,outputdir='+self.output_directory+\
'/,processors='+str(self.processors)+')" > $3', cmd_format='{EXE} {IN} {OUT}')
'/,processors='+str(self.processors)+')" > $3 2>$4', cmd_format='{EXE} {IN} {OUT}')
chimerauchime = MultiMap(chimerauchime, inputs=[self.fasta_files,self.reference_files], \
outputs=[self.stdout,self.uchime_chimera_files,self.uchime_accnos_files])
outputs=[self.stdout,self.stderr,self.uchime_chimera_files,self.uchime_accnos_files])
elif self.names_files and not self.groups_files:
chimerauchime = ShellFunction(self.get_exec_path("mothur") + ' "#chimera.uchime(fasta=$1,name=$2,outputdir='+self.output_directory+\
'/,processors='+str(self.processors)+')" > $3', cmd_format='{EXE} {IN} {OUT}')
'/,processors='+str(self.processors)+')" > $3 2>$4', cmd_format='{EXE} {IN} {OUT}')
chimerauchime = MultiMap(chimerauchime, inputs=[self.fasta_files,self.names_files], \
outputs=[self.stdout,self.uchime_chimera_files,self.uchime_accnos_files])
outputs=[self.stdout,self.stderr,self.uchime_chimera_files,self.uchime_accnos_files])
else:
chimerauchime = ShellFunction(self.get_exec_path("mothur") + ' "#chimera.uchime(fasta=$1,name=$2,group=$3,outputdir='+self.output_directory+\
'/,processors='+str(self.processors)+')" > $4', cmd_format='{EXE} {IN} {OUT}')
'/,processors='+str(self.processors)+')" > $4 2>$5', cmd_format='{EXE} {IN} {OUT}')
chimerauchime = MultiMap(chimerauchime, inputs=[self.fasta_files,self.names_files,self.groups_files], \
outputs=[self.stdout,self.uchime_chimera_files,self.uchime_accnos_files])
outputs=[self.stdout,self.stderr,self.uchime_chimera_files,self.uchime_accnos_files])
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