Re: [galaxy-dev] Bowtie2 index building

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 wrote: > > Hi, > > it seems that your Docker Box only gets 1GB :( > > please re-check the configs. > Sorry to be

Re: [galaxy-dev] Bowtie2 index building

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. > > T

Re: [galaxy-dev] Bowtie2 index building

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 mailto:dktan...@hotmail.com>> wrote: Hi Björn, If I do docker stats: CONTAINER CPU %

Re: [galaxy-dev] Bowtie2 index building

Hi Björn, If I do docker stats: CONTAINER CPU % MEM USAGE / LIMIT MEM % NET I/O BLOCK I/O PIDS dd4da10c0a546.16% 690.9MiB / 995.8MiB 69.38% 158kB / 785kB 11.4GB / 81MB 106 And, after

Re: [galaxy-dev] Bowtie2 index building

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 cor

[galaxy-dev] 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

[galaxy-dev] bowtie2 indexes & errors

Hi, I observe next error: [2017-03-21 10:30:56] Beginning TopHat run (v2.1.0) --- [2017-03-21 10:30:56] Checking for Bowtie Bowtie version:2.2.5.0 [2017-03-21 10:30:56] Checking for Bowtie index files (genome).. Error: Could not

[galaxy-dev] bowtie2 data_manager issue

I am indexing reference genomes for bowtie2/tophat2, using the corresponding data manager. I am getting some successful indexes and others are giving an error. For the successful ones I see the genomes are appearing in the "built in index" drop down for both bowtie2 and tophat2. For the unsuccessfu

Re: [galaxy-dev] Bowtie2

Awesome! Glad you got it to work. Am 13.01.2016 um 21:19 schrieb Laforest, Martin: > Seems to work after server reboot... > > Thanks > > Martin > > De : Laforest, Martin > Envoyé : 13 janvier 2016 10:00 > À : 'galaxy-dev@lists.galaxyproject.org' > Objet : RE: Bowtie2 > > Oups I made a mistake

Re: [galaxy-dev] Bowtie2

Seems to work after server reboot... Thanks Martin De : Laforest, Martin Envoyé : 13 janvier 2016 10:00 À : 'galaxy-dev@lists.galaxyproject.org' Objet : RE: Bowtie2 Oups I made a mistake I have problems with the tophat wrapper, not bowtie. Bowtie runs fine... Tophat - fast splice junction

Re: [galaxy-dev] Bowtie2

Oups I made a mistake I have problems with the tophat wrapper, not bowtie. Bowtie runs fine... Tophat - fast splice junction mapper for RNA-Seq reads 4eb3c3beb9c7 Devteam Packages package_bowtie_2_2_5 and package_2_0_14 are installed... Thanks Martin De : Laforest, Martin Envoyé : 13 janv

[galaxy-dev] Bowtie2

Hello, Please excuse my simple question since I'm a newbie... I've searched the mailing list but did not find the appropriate answer... I have a new Galaxy installation. I installed the tool "Bowtie2: Fast and sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool apparen