Unable to overcome troubles in whole exome analysis

Hi, I am working on whole exome sequencing data whose pipeline has been standardized in the lab as such –

Align with bwa-mem –> SortSam based on coordinates with Picard –> MarkDuplicates –> Remove sequencing duplicates –> Variant calling –> BQSR –> Variant calling –> Annotate with annovar

When I started working on this (on our institutional server), I had not created a java temp directory and it was working fine, but over time I started receiving Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device' 'Caused by: java.io.IOException: No space left on device errors, because of which I created the java temp directory. Upon doing so I am receiving the following error –

Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once.  1: null:A01223:29:HY2N7DMXX:2:2306:22562:23375
    at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:133)
    at htsjdk.samtools.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:86)
    at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.remove(DiskBasedReadEndsForMarkDuplicatesMap.java:61)
    at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:528)
    at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:232)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

I tried working on it by adding read groups, fixing mate pair information, removing duplicates with tools apart from Picard, but nothing seems to be helping. I tried to remove the java temp directory, but I received Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device' 'Caused by: java.io.IOException: No space left on device yet again. I am looking for a solution as early as possible.

Thanks in advance 🙂