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 :)