Hi Lilach,

The problem with this analysis probably has to do with a mismatch between the genomes: the intervals obtained from UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run.

UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'.

Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 with UCSC hg19 for an explanation. Reference genomes must be exact in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other.

Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try.

Good luck with the re-run!

Jen
Galaxy team

On 6/18/12 4:42 AM, Lilach Friedman wrote:

Hi,
I am trying to used Depth of Coverage to see the coverages is specific intervals.
The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals.

I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM)
and the intervals file (in advanced GATK options).
The consensus genome is hg_g1k_v37.

I got the following error message:

An error occurred running this job: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0):
##### ERROR The invalid argume

Is it a bug, or did I do anything wrong?

I will be grateful for any help.

Thanks!
Lilach
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