ambiguous redirect error

upendra_35 · 12-12-2012, 12:56 PM

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

Then i modified it to run as below

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

But still i am getting the error. Could somebody help me with this.....

Thanks
Upendra

shivaa · 12-12-2012, 01:08 PM

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)
example# EDITOR=vi; export EDITOR  (sh/bash style)
example# echo $EDITOR
example# <your_code>

upendra_35 · 12-12-2012, 03:33 PM

Quote:

Originally Posted by shivaa

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)
example# EDITOR=vi; export EDITOR  (sh/bash style)
example# echo $EDITOR
example# <your_code>

I retried but still getting the same error.....

AnanthaP · 12-12-2012, 07:51 PM

(1) Anything to do with *fq?
(2) Try putting DOUBLE QUOTES around all variables when used in directory/file name constructs.

OK