Re: [galaxy-dev] BWA missing index on reference genome
Hey, now I'm stuck with the calculate SA coordinate. Segmenation fault. Google tells me that it could be a problem with -space (I have 4GB left) -the version I use. (I use 0.5.9 and did a succesful alignment with 0.7.5a, but the tool shed says 0.5.9, hence could I just change to the current version, with which I did a succesful alignment?) Best Moritz On 26 July 2013 16:15, Jennifer Jackson wrote: > Hi Moritz, > > Pls see below > > On Jul 26, 2013, at 6:37 AM, Moritz Juchler < > juch...@stud.uni-heidelberg.de> wrote: > > Hey, > > 1 I installed Galaxy locally. > 2 I also have BWA installed and then used the > 3 shed repository to get the bwa wrapper. > 4 I have the reference genome: > >> -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict >> -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta >> -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb >> -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann >> -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt >> -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai >> -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac >> -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa > > > 5 and I changed the bwa_index and bw_index_color.loc to the path > /genedata/human_genome_GRCh37/hg19.fa > > > This is the problem - the path must point to the full name of the fasta > file. In your case "human_g1kv_v37.fasta". > > Using the name without the fasta as the base name in other fields as the > unique "dbkey" is a good practice. > > Hopefully this helps, > > Jen > Galaxy team > > > > 6 This is my *$PATH* > >> trr@portalmoritz:~> echo $PATH >> >> /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 > > > Is there anything I am missing? I would be glad about some help. > Best > Moritz > > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > Jennifer Hillman-Jackson > Galaxy Support & Training > http://galaxyproject.org > ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BWA missing index on reference genome
I solved it so far :) Thanks for your help. On 26 July 2013 16:15, Jennifer Jackson wrote: > Hi Moritz, > > Pls see below > > On Jul 26, 2013, at 6:37 AM, Moritz Juchler < > juch...@stud.uni-heidelberg.de> wrote: > > Hey, > > 1 I installed Galaxy locally. > 2 I also have BWA installed and then used the > 3 shed repository to get the bwa wrapper. > 4 I have the reference genome: > >> -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict >> -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta >> -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb >> -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann >> -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt >> -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai >> -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac >> -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa > > > 5 and I changed the bwa_index and bw_index_color.loc to the path > /genedata/human_genome_GRCh37/hg19.fa > > > This is the problem - the path must point to the full name of the fasta > file. In your case "human_g1kv_v37.fasta". > > Using the name without the fasta as the base name in other fields as the > unique "dbkey" is a good practice. > > Hopefully this helps, > > Jen > Galaxy team > > > > 6 This is my *$PATH* > >> trr@portalmoritz:~> echo $PATH >> >> /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 > > > Is there anything I am missing? I would be glad about some help. > Best > Moritz > > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > Jennifer Hillman-Jackson > Galaxy Support & Training > http://galaxyproject.org > ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BWA missing index on reference genome
Hi Moritz, Pls see below On Jul 26, 2013, at 6:37 AM, Moritz Juchler wrote: > Hey, > > 1 I installed Galaxy locally. > 2 I also have BWA installed and then used the > 3 shed repository to get the bwa wrapper. > 4 I have the reference genome: >> -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict >> -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta >> -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb >> -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann >> -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt >> -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai >> -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac >> -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa > > 5 and I changed the bwa_index and bw_index_color.loc to the path > /genedata/human_genome_GRCh37/hg19.fa This is the problem - the path must point to the full name of the fasta file. In your case "human_g1kv_v37.fasta". Using the name without the fasta as the base name in other fields as the unique "dbkey" is a good practice. Hopefully this helps, Jen Galaxy team > > 6 This is my $PATH >> trr@portalmoritz:~> echo $PATH >> /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 > > Is there anything I am missing? I would be glad about some help. > Best > Moritz > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ Jennifer Hillman-Jackson Galaxy Support & Training http://galaxyproject.org___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] BWA missing index on reference genome
Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome: > -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict > -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta > -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb > -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann > -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt > -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai > -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac > -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa 5 and I changed the bwa_index and bw_index_color.loc to the path /genedata/human_genome_GRCh37/hg19.fa 6 This is my *$PATH* > trr@portalmoritz:~> echo $PATH > > /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 Is there anything I am missing? I would be glad about some help. Best Moritz ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
