Question: RealignerTarget Creator in Galaxy
0
gravatar for arunnatrajanravi
2.8 years ago by
Luxembourg
arunnatrajanravi0 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 ------------------------------------------------------------------------------------------

The thing is, in galaxy the realignerTarget creator didn't recognize my 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 for your precious help,

Aaron5664

realigner fasta gatk • 1.0k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by arunnatrajanravi0
0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

This may sound simple, but double check that the input fasta is actually labeled with the datatype "fasta".

How to do this is in our wiki here:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

And all about Custom Reference genomes is here, including a brand new screencast:
http://wiki.galaxyproject.org/Learn/CustomGenomes

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson23k
1

Hi Jen,

as reference: https://www.biostars.org/p/135908/

ADD REPLYlink written 2.8 years ago by Bjoern Gruening4.8k

hi,

Does it mean that I should just rename my reference file?

Well, as my ref genome was already in fasta format. I didn't convert it. Then, the other thing that I did was to download this ref genome from Data Libraries > GATK > bundle... I am wondering if I did it correctly.

Aaron5664

ADD REPLYlink written 2.8 years ago by arunnatrajanravi0
1

Hello, The dataset does not need to be renamed, but the metadata must be assigned correctly for tools to function correctly. In this case, the important metadata is "datatype". The first link explains how to assign. If working on the public Main Galaxy instance at http://usegalaxy.org, and are using the fasta file from this Data Library hosted on Main, and imported it directly into a history, it should be good to go. But, since you are having trouble, double check the datatype and the format of all inputs. All must be based on the same exact reference genome including the sequence identifiers. It sounds as if the dbSNP dataset is, but double checking is worth it - format is the most common reason for tool issues. Your error above is because the default genome (hg_g1k_b37) was used and this is a mismatch for at least the dbSNP dataset. Best, Jen, Galaxy team

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson23k
0
gravatar for arunnatrajanravi
2.8 years ago by
Luxembourg
arunnatrajanravi0 wrote:

Hi,

Thank you for your help. It's working now. But, I am getting the following error:

"""

This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help.

"""

What should I do?

Aaron5664

ADD COMMENTlink written 2.8 years ago by arunnatrajanravi0

Are you running your jobs on a cluster? Do you have admin permissions?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Bjoern Gruening4.8k

Hi,

I got this message from a galaxy server.

ADD REPLYlink written 2.8 years ago by arunnatrajanravi0

Hi Aaron5664,

If you click the bug link on the expanded dataset, optionally add some text about what you are trying to do, then click "Report", we can go ahead and review the memory allocations being given to this tool. Thanks.

ADD REPLYlink written 2.8 years ago by Daniel Blankenberg ♦♦ 1.7k

Ok. I'll do it now.

Thank you very much.

ADD REPLYlink written 2.8 years ago by arunnatrajanravi0
0
gravatar for arunnatrajanravi
2.8 years ago by
Luxembourg
arunnatrajanravi0 wrote:

Hi everyone,

I have an other question. I installed galaxy locally and I am starting to run galaxy.

I tried to upload the references (you know hg19, dbsnp, bundle...etc). It took two days and I have nothing in my libraries. I followed the tutorial on galaxy :

https://wiki.galaxyproject.org/Admin/DataLibraries/Libraries

Is there another way to upload? like copy/paste to some location as it's on my system?...

Best Regards,

ADD COMMENTlink written 2.8 years ago by arunnatrajanravi0
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