LinuxQuestions.org
Help answer threads with 0 replies.
Go Back   LinuxQuestions.org > Forums > Linux Forums > Linux - Newbie
User Name
Password
Linux - Newbie This Linux forum is for members that are new to Linux.
Just starting out and have a question? If it is not in the man pages or the how-to's this is the place!

Notices


Reply
  Search this Thread
Old 12-12-2012, 12:56 PM   #1
upendra_35
LQ Newbie
 
Registered: Oct 2012
Posts: 21

Rep: Reputation: Disabled
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
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

Last edited by upendra_35; 12-12-2012 at 12:59 PM.
 
Old 12-12-2012, 01:08 PM   #2
shivaa
Senior Member
 
Registered: Jul 2012
Location: Grenoble, Fr.
Distribution: Sun Solaris, RHEL, Ubuntu, Debian 6.0
Posts: 1,800
Blog Entries: 4

Rep: Reputation: 286Reputation: 286Reputation: 286
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>
 
Old 12-12-2012, 03:33 PM   #3
upendra_35
LQ Newbie
 
Registered: Oct 2012
Posts: 21

Original Poster
Rep: Reputation: Disabled
Quote:
Originally Posted by shivaa View Post
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.....
 
Old 12-12-2012, 07:51 PM   #4
AnanthaP
Member
 
Registered: Jul 2004
Location: Chennai, India
Distribution: UBUNTU 5.10 since Jul-18,2006 on Intel 820 DC
Posts: 828

Rep: Reputation: 200Reputation: 200Reputation: 200
(1) Anything to do with *fq?
(2) Try putting DOUBLE QUOTES around all variables when used in directory/file name constructs.

OK
 
  


Reply


Thread Tools Search this Thread
Search this Thread:

Advanced Search

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is Off
HTML code is Off



Similar Threads
Thread Thread Starter Forum Replies Last Post
bash returns ambiguous redirect with date in filename rstoutmna Programming 5 09-13-2011 07:37 PM
[SOLVED] bash ambiguous redirect wakatana Programming 2 03-09-2011 09:35 AM
Ambiguous output redirect XFox Linux - Newbie 5 10-17-2003 07:29 PM
Ambiguous Redirect Error AMMullan Linux - General 1 10-01-2003 08:39 PM
ambiguous redirect? cuss Linux - General 4 03-06-2003 10:58 AM


All times are GMT -5. The time now is 04:49 AM.

Main Menu
Advertisement
My LQ
Write for LQ
LinuxQuestions.org is looking for people interested in writing Editorials, Articles, Reviews, and more. If you'd like to contribute content, let us know.
Main Menu
Syndicate
RSS1  Latest Threads
RSS1  LQ News
Twitter: @linuxquestions
Facebook: linuxquestions Google+: linuxquestions
Open Source Consulting | Domain Registration