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Old 02-19-2014, 06:39 AM   #1
thh32
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Location: UK

Join Date: Feb 2014
Posts: 60
Default SOAPdenovo2 Ambiguous output redirect.

Currently using SOAPdenovo2 and used submission form below:

Code:
#!/bin/bash
#$ -cwd
#$ -N SOAPdenovo2
#$ -e /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOAPdenovo2.error
#$ -o /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOApdenovo2.output
#$ -M [email protected]
#$ -q intel.q

#step1
/cm/shared/apps/soapdenovo2/r240 sparse_pregraph -s /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOAPdenovo2_config_file -K 35 -R -o graph_prefix 1>pregraph.log 2>pregraph.err
#step2
/cm/shared/apps/soapdenovo2/r240 contig -g graph_prefix -R 1>contig.log 2>contig.err
#step3
/cm/shared/apps/soapdenovo2/r240 map -s config_file -g graph_prefix 1>map.log 2>map.err
#step4
/cm/shared/apps/soapdenovo2/r240 scaff -g graph_prefix -F 1>scaff.log 2>scaff.err
However this failed instantly and produced a .error and .output file, the .error file contained "Ambiguous output redirect." and the .output file contained "Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell."

Anyone know why?
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Old 02-19-2014, 08:29 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
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I think you are using the redirects incorrectly in your command lines above: http://forums.fedoraforum.org/showthread.php?t=219335
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