On Mon, 20 Apr 2020, Pedro Hollanda Carvalho wrote:
Hi, could anyone help me with this?
I'm trying to convert SAM to BAM using samtools view and I have the
following error message
$ sudo samtools view -bS Kp01.sam > Kp01.bam
-bash: Kp01.bam: Permission denied
Judging from the error message, you either don't have permission to create
Kp01.bam in the current directory, or one already exists that you can't
overwrite. Note that the '> Kp01.bam' part of the command above is being
run as yourself, and not as root (via 'sudo').
Also, *** you should not be running samtools as root via sudo ***. It is
not designed to be used that way. Instead, you should use sudo (if
necessary) to create a directory where your normal account has write
permissions, and then use that to store the results from samtools.
For example (assuming directory 'output' does not exist:
sudo mkdir output
sudo chown `whoami`.`groups | awk '{ print $1 }'` output
samtools view -bS Kp01.sam > output/Kp01.bam
I have already tried from different locations and used sudo command but
always got the same error
You probably need to check permissions of the various files and
directories that you have made. If you have been using 'sudo' you may now
have a mixture of ownership, which is likely to be painful. In general,
you shouldn't use 'sudo' unless you really have to.
Rob Davies r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs., Tel. +44 (1223) 834244
CB10 1SA, U.K. Fax. +44 (1223) 494919
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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