ambiguous redirect error
I am getting "ambiguous redirect error" when i try to run the below command.
Code:
for lane in 0{1..5} 0{8..9} 11 12 ; do ./bwa_tophat_final.pl --threads 12 --out $map_dir/$fq_id.$lane --bwa_n 0.04 --bwa_db db/B.rapa_genome_sequence_0830.fa --fq $fq_dir/$lane/*fq --fq_id $fq_id.$lane --bowtie_db db/B.rapa_genome_sequence_0830 --ref_fa db/B.rapa_genome_sequence_0830.fa --ref_id Brapa0830 > $map_dir/$fq_id.$lane.bwa_tophat.log 2> $map_dir/$fq_id.$lane.bwa_tophat.err & done Code:
for lane in 0{1..5} 0{8..9} 11 12 ; do ./bwa_tophat_final.pl --threads 12 --out $map_dir/$fq_id.$lane --bwa_n 0.04 --bwa_db db/B.rapa_genome_sequence_0830.fa --fq $fq_dir/$lane/*fq --fq_id $fq_id.$lane --bowtie_db db/B.rapa_genome_sequence_0830 --ref_fa db/B.rapa_genome_sequence_0830.fa --ref_id Brapa0830 > $map_dir/$fq_id.$lane.bwa_tophat.log >& $map_dir/$fq_id.$lane.bwa_tophat.err & done Thanks Upendra |
Such issue comes if your default EDITOR is not set, so once set it as follow, and try again:
Code:
example# setenv EDITOR vi (csh/tcsh shell) |
Quote:
|
(1) Anything to do with *fq?
(2) Try putting DOUBLE QUOTES around all variables when used in directory/file name constructs. OK |
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