Hi All,

I am having problems using GATK Indel Realigner. We installed our own galaxy 
instance on a VM server and configured it to submit jobs through DRMAA to the 

The first error I got is:


ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK 
Key file. Please see 
 for more information and instructions on how to obtain a key.


I solved this by modifying the "indel_realigner.xml" file and changed the -rt 
"NO_ET" to "-et STANDARD".

Then comes the second the error as below:


ERROR MESSAGE: Invalid command line: Failed to load reference dictionary


Stdout has:


[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM 


The "dataset.dat" file has the following:


INFO  09:17:58,332 RodBindingArgumentTypeDescriptor - Dynamically determined 
type of /tmp/tmp-gatk-2gGVA2/gatk_target_intervals.bed to be BED

INFO  09:17:58,452 GenomeAnalysisEngine - Strictness is SILENT

WARN  09:17:58,502 FSLockWithShared - WARNING: Unable to lock file 
/work/galaxy/galaxy/genomes/mm9/picard/mm9.dict: Function not implemented.

INFO  09:17:58,504 ReferenceDataSource - Unable to create a lock on dictionary 
file: Function not implemented

INFO  09:17:58,505 ReferenceDataSource - Treating existing dictionary file as 

WARN  09:17:58,507 FSLockWithShared - WARNING: Unable to lock file 
/work/galaxy/galaxy/genomes/mm9/picard/mm9.fa.fai: Function not implemented.

INFO  09:17:58,509 ReferenceDataSource - Unable to create a lock on index file: 
Function not implemented

INFO  09:17:58,510 ReferenceDataSource - Treating existing index file as 


I don't have any bio background and lost track of the error messages. Is this 
error caused by the Galaxy GATK wrapper or the input data files? I got those 
input files from my colleague who used to run them successfully on another 
older Galaxy server. That makes me wonder if there is something with our GATK 

My apologies if asking this question in the wrong place. Any suggestion is 


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