Hi every one, Tools that utilize BWA-MEM (e.g. BwaSpark, PathSeqBwaSpark) require an index image file of the reference sequences. BwaMemIndexImageCreator tool generates the image file (.img) from a reference FASTA file. I am trying to create a BWA-MEM index image file for use with GATK BWA tools StructuralVariationDiscoveryPipelineSpark.

I am indexed the human reference genome with BWA with following command:

  $bwa index NGS/GRef/bwa-GRef/gr.fa
  $samtools faidx NGS/GRef/bwa-GRef/gr.fa

then, run the BwaMemIndexImageCreator tool for creation of .img file with following command:

$java -DGATK_STACKTRACE_ON_USER_EXCEPTION=’true’ -Xms10g -jar NGS/soft/gatk/gatk-package-4.0.8.1-local.jar BwaMemIndexImageCreator -I NGS/GRef/bwa-GRef/gr.fa -O GRef/bwa-GRef/gr.fa.img

but it fails to generate .img file with following error:

20:38:34.953 INFO  NativeLibraryLoader - Loading libgkl_compression.so
from
jar:file:/home/novingenetic/NGS/soft/gatk/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 20:38:36.291 INFO  BwaMemIndexImageCreator -
------------------------------------------------------------ 20:38:36.291 INFO  BwaMemIndexImageCreator - The Genome Analysis
Toolkit (GATK) v4.0.8.1 20:38:36.292 INFO  BwaMemIndexImageCreator -
For support and documentation go to
https://software.broadinstitute.org/gatk/ 20:38:36.292 INFO 
BwaMemIndexImageCreator - Executing as novingenetic@novingenetics on
Linux v4.15.0-58-generic amd64 20:38:36.293 INFO 
BwaMemIndexImageCreator - Java runtime: OpenJDK 64-Bit Server VM
v1.8.0_222-8u222-b10-1ubuntu1~18.04.1-b10 20:38:36.293 INFO 
BwaMemIndexImageCreator - Start Date/Time: August 26, 2019 8:38:34 PM
IRDT 20:38:36.294 INFO  BwaMemIndexImageCreator -
------------------------------------------------------------ 20:38:36.294 INFO  BwaMemIndexImageCreator -
------------------------------------------------------------ 20:38:36.295 INFO  BwaMemIndexImageCreator - HTSJDK Version: 2.16.0
20:38:36.296 INFO  BwaMemIndexImageCreator - Picard Version: 2.18.7
20:38:36.296 INFO  BwaMemIndexImageCreator - HTSJDK
Defaults.COMPRESSION_LEVEL : 2 20:38:36.296 INFO 
BwaMemIndexImageCreator - HTSJDK
Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 20:38:36.297 INFO 
BwaMemIndexImageCreator - HTSJDK
Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 20:38:36.297 INFO 
BwaMemIndexImageCreator - HTSJDK
Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 20:38:36.297 INFO 
BwaMemIndexImageCreator - Deflater: IntelDeflater 20:38:36.298 INFO 
BwaMemIndexImageCreator - Inflater: IntelInflater 20:38:36.298 INFO 
BwaMemIndexImageCreator - GCS max retries/reopens: 20 20:38:36.298
INFO  BwaMemIndexImageCreator - Using google-cloud-java fork
https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
20:38:36.298 INFO  BwaMemIndexImageCreator - Initializing engine
20:38:36.299 INFO  BwaMemIndexImageCreator - Done initializing engine
[bwa_index] Pack FASTA... 21.34 sec [bwa_index] Construct BWT for the
packed sequence... Killed

I was wondering if any one knows how I can generate the .img file?

• operation system: linux ubuntu v18

• java version: openjdk version "1.8.0_222"

• bwa version: 0.7.17-r1188

• gatk version: gatk-4.0.8.1