Bowtie2 index building
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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<mailto: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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Also, I am running this container on a Mac Pro using Kitematic and I have docker preference set to use 12 cores and 64 GB RAM. Thanks, Deepak On Aug 11, 2017, at 9:54 AM, Deepak Tanwar <dktanwar@hotmail.com<mailto: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<mailto: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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Hi, it seems that your Docker Box only gets 1GB :( please re-check the configs. Sorry to be not more helpful! Bjoern On 11.08.2017 15:55, Deepak Tanwar wrote:
Also, I am running this container on a Mac Pro using Kitematic and I have docker preference set to use 12 cores and 64 GB RAM.
Thanks, Deepak
On Aug 11, 2017, at 9:54 AM, Deepak Tanwar <dktanwar@hotmail.com <mailto: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 <mailto: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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Hi Björn, That’s right! It was quiet strange. I need to extend the memory and cores usage via command line. Thank you so much! Deepak
On Aug 11, 2017, at 10:00, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
it seems that your Docker Box only gets 1GB :(
please re-check the configs. Sorry to be not more helpful! Bjoern
On 11.08.2017 15:55, Deepak Tanwar wrote:
Also, I am running this container on a Mac Pro using Kitematic and I have docker preference set to use 12 cores and 64 GB RAM.
Thanks, Deepak
On Aug 11, 2017, at 9:54 AM, Deepak Tanwar <dktanwar@hotmail.com <mailto: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 <mailto: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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
participants (2)
-
Björn Grüning -
Deepak Tanwar