On Aug 11, 2017, at 9:54 AM, Deepak Tanwar <dktanwar@hotmail.com> wrote:

Hi Björn,

If I do docker stats:

CONTAINER           CPU %               MEM USAGE / LIMIT     MEM %               NET I/O             BLOCK I/O           PIDS

dd4da10c0a54        6.16%               690.9MiB / 995.8MiB   69.38%              158kB / 785kB       11.4GB / 81MB       106

And, after ssh into docker machine:

Filesystem                Size      Used Available Use% Mounted on

tmpfs                   896.2M    186.6M    709.6M  21% /

tmpfs                   497.9M    476.0K    497.4M   0% /dev/shm

/dev/sda1               282.7G     14.9G    253.2G   6% /mnt/sda1

cgroup                  497.9M         0    497.9M   0% /sys/fs/cgroup

Users                   931.0G    683.8G    247.2G  73% /Users

/dev/sda1               282.7G     14.9G    253.2G   6% /mnt/sda1/var/lib/docker/aufs

Best regards,

Deepak

On Aug 11, 2017, at 9:39 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:

Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak



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