permissions of 1000genomes data messed up

[Jan Aerts]

Hi all,

I will be using cloudbiolinux with 1000 Genomes data for teaching starting the end of this week. I created a new instance on EC2 region US-East (searched for "1000HumanGenomes"). When logging into that server, I indeed see a directory /mnt/1000genomes. The permissions in this directory are however messed up:

-r--r--r-- 1 root   root                4092699 2012-03-27 17:51 alignment.index

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 alignment_indices

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 CHANGELOG

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 changelog_details

---------- 1 root   root               43157492 2012-05-04 17:47 current.tree

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 data

-r--r--r-- 1 root   root                2049291 2012-03-12 20:13 exome.alignment.index

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 phase1

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 pilot_data

-r--r--r-- 1 root   root                  16244 2012-03-27 19:47 README.alignment_data

-r--r--r-- 1 root   root                   8408 2011-04-04 13:52 README.ftp_structure

-r--r--r-- 1 ubuntu ubuntu                 2082 2009-08-14 12:58 README.pilot_data

-r--r--r-- 1 root   root                   1506 2012-01-11 15:12 README.populations

-r--r--r-- 1 ubuntu ubuntu                 6548 2011-07-23 21:03 README.sequence_data

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 release

-r--r--r-- 1 root   root               33690740 2012-04-20 15:06 sequence.index

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 sequence_indices

---------- 1 root   root   18446744073709551615 1969-12-31 23:59 technical

As you can see, the permissions for all directories are set to "000". A "sudo chmod 755 pilot_data" gives me an Input/output error. Rebooted the EC2 instance in the hope that that would help, but to no avail...

Any help much appreciated!

Thanks,

jan.

[agbiotec]

Hi Jan,

  this volume is actually a public one from the 1000 genomes project - it was created by them, see paper here:

http://www.nature.com/nmeth/journal/v9/n5/full/nmeth.1974.html

I just wrote a script to mount it on the instance via sshfs. Since the volume is owned by the 1000 genomes project, 

it makes sense to have only read permissions (I fwd-ed your email to them, let's see what they think).

You can mount a second volume which you create yourself and have write permissions:

http://docs.amazonwebservices.com/AWSEC2/latest/UserGuide/ebs-creating-volume.html

http://docs.amazonwebservices.com/AWSEC2/latest/UserGuide/ebs-using-volumes.html

On that second volume you could copy some of the genome data, or have your data processing apps read 

from the 1000 genomes read-only volume, and write output to the second one.

Let me know if you need any more help on these.

 cheers,

Ntino

[agbiotec]

Update: it's actually 1000 Genomes S3 buckets which are readable by all, and my scripts

mounts them via s3fs. Still read-only as I mentioned below since the buckets are owned by them.

 Ntino

[agbiotec]

---------- Forwarded message ----------

From: Preuss, Don (NIH/NLM/NCBI) [E] 

Date: Fri, Jun 1, 2012 at 12:34 PM

Subject: RE: permissions of 1000genomes data messed up

At the time (May 6th) there was an issue. Have you tried this again recently?

 

(And we do apologize for the problem at the beginning of the month)

 

Donp

On Sunday, May 6, 2012 9:29:32 AM UTC-4, Jan Aerts wrote:

[Jan Aerts]

Hey Don,

I actually shut down that EC2 server yesterday because the course finished last week... In the end we only used some files that we needed, and didn't need to access that volume. So I have no idea if the issue is solved at the moment... :-/

jan.

================================
Dr Jan Aerts
Assistant Professor
Faculty of Engineering - ESAT/SCD
Kasteelpark Arenberg 10 bus 2446
3001 Leuven-Heverlee
Tel: +32 16 321053
Fax: +32 16 321970 

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