Question: (Closed) Galaxy Based GATK Realigner Target Creator
0
gravatar for arunnatrajanravi
3.6 years ago by
France
arunnatrajanravi30 wrote:

Hi,

I am just starting to use galaxy. I am having a trouble using the GATK tool called Realigner Target creator.

What should I do?

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version exported): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Input files /galaxy-repl/main/scratch/tmp-gatk-P3rMwA/input_dbsnp_0.vcf and reference have incompatible contigs: No overlapping contigs found.
##### ERROR   /galaxy-repl/main/scratch/tmp-gatk-P3rMwA/input_dbsnp_0.vcf contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]
##### ERROR   reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1]
##### ERROR ------------------------------------------------------------------------------------------
tutorial galaxy gatk • 1.7k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by arunnatrajanravi30

Hello arunnatrajanravi!

We believe that this post does not fit the main topic of this site.

This post belongs on http://biostar.usegalaxy.org/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.6 years ago by RamRS19k
1
gravatar for Björn
3.6 years ago by
Björn650
Germany
Björn650 wrote:

Hi,

Galaxy related questions are usually better to ask here: http://biostar.usegalaxy.org/

Nevertheless, this does not seem like a Galaxy problem. It seems you have used different reference genomes. One set of genome (annotations) is based on the chromosome naming scheme (1,2,3,4) and the other is UCSC based (chr1, chr2, chr3). You need to unify this, otherwise GATK can not map between both sets.

Hope this helps,

Bjoern

ADD COMMENTlink written 3.6 years ago by Björn650
0
gravatar for arunnatrajanravi
3.6 years ago by
France
arunnatrajanravi30 wrote:

@Bjoern

Thank you,

if needed, I'll repost it to link you gave me. Thank you really for the information. I have to say that I am new to this forum. The thing is, in galaxy the realignerTarget creator didn't recognize the reference genome (i.e.) ucsc.hg19.fasta. I am not getting why this is not working.

I am using dbsnp_138.hg19.vcf in the known option.

Thank you,

Aaron

ADD COMMENTlink written 3.6 years ago by arunnatrajanravi30
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