Currently using SOAPdenovo2 and used submission form below:
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?
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
Thus no job control in this shell."
Anyone know why?
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