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
[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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