Joshua and Philipe thanks for the input. I was able to run the GATK in another pipeline but does not serve my purpose. It was FASTQ groomer followed by BWA alignment with human_g1k_v37 with the read groups. It produced a SAM file which I put into GATK pipeline with option "use as BAM(SAM file)". Once it started running, it kept going. But several issues with it. GATK best practices recommend removing the duplicates with Picard before this but after using Picard this output wont work in galaxy GATK. The second issue is if I align with Hg 19 because this is what I have been working with, even if I provide the reference H19 from history (uploaded) GATK does not work.
All I needed was base recalibration and indel realignment so I decided to do these before running the picard duplicate removal tool and run everything with human_g1k_v37. It worked from base recalibration then indel realignment band then Picard duplicate removal. But I needed to run mpileup on this output. A very interesting thing I found that even though everything in this pipeline was with human_g1k_v37 but the mpileup will run only with Hg19. As I cannot rely on such a twisted pipeline so essentially cannot use GATK in galaxy. ________________________________________ From: Joshua Orvis [jor...@gmail.com] Sent: Tuesday, December 11, 2012 5:34 PM To: Philipe Moncuquet Cc: Farooq,Umar (res); galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] GATK Not running I'm having some problems with GATK as well, but do have a functional pipeline that uses the following GATK tools in Galaxy: - Realigner Target Creator - Indel Realigner - Unified Genotyper - Variant Filtration The main problem I'm having with them is that it seems I need to run the fasta/fastq groomer on all inputs before starting, and if I attempt to use the 'advanced' options on either of the last two steps above it fails immediately every time with a command-line option parsing error. I plan on digging into the wrapper script in the coming days in an attempt to correct this, which is currently attributed to Dan Blankenberg. I'm relatively new to Galaxy development though and don't know where to submit my updates though should I fix any of these problems. Joshua On Tue, Dec 11, 2012 at 4:26 PM, Philipe Moncuquet <philippe.m...@gmail.com<mailto:philippe.m...@gmail.com>> wrote: Hi, I have encountered the same kind of errors. When I update the loc files link to GATK, some of the tools display the reference genomes I added and some not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. GATK don't really care because they are not supporting it any more, even documentation has disappeared. And I understand that galaxy developers have other stuff to do than supporting a tool that will disappear because it's not open source any more. I don't know what tool could replace the recalibration process done by GATK and don't know how to correct bugs neither. Any suggestions ? Philippe 2012/12/12 Farooq,Umar (res) <ufar...@resident.uchc.edu<mailto:ufar...@resident.uchc.edu>> Hi, I am trying to incorporate GATK in my pipeline but not been able to make it work. I aligned my data with Hg 19 and then ran sam tool filter and then picard duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in galaxy to run this pipeline. But for some reason GATK tool for base recalibration will not accept this output file. I wonder if there is sorting or indexing issue but how to fix this in galaxy. An error occurred running this job: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp Thanks, Umar ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
