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Facing an issue in IlluminaBasecallsToSam module; working in Ubuntu18 but not working in Centos7

Krithika_SubramanianKrithika_Subramanian BangaloreMember
edited November 2019 in Ask the GATK team

Dear GATK Support Team,

We are facing issues while running IlluminaBasecallsToSam module in Centos7. We tried running each Lane separately to generate unaligned BAM. We got "OutOfMemory: Java heap space" (Attached error image).

The below is the Lane1 command line arguments.

___gatk IlluminaBasecallsToSam --BASECALLS_DIR Data/Intensities/BaseCalls/ --BARCODES_DIR Barcode1_dir/ --RUN_BARCODE Lane1 --LIBRARY_PARAMS library_param.txt --LANE 1 --NUM_PROCESSORS "num" --READ_STRUCTURE "pattern"___

The above command working in Ubuntu-18. Our production servers have Centos7, so kindly help us to fix this issue on Centos7.

Thank you
Krithika S


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