Hello,
I'm trying to go through the drop-seq pipeline, but unfortunately I'm stuck on a seemingly insurmountable technical issue:
I enter this command to merge BAM files:
[Mon Mar 06 13:23:14 EST 2017] picard.sam.MergeBamAlignment UNMAPPED_BAM=./unaligned_mc_tagged_polyA_filtered.bam ALIGNED_BAM=[./aligned.sorted.bam] OUTPUT=./merged.bam REFERENCE_SEQUENCE=/home/con/Alex/mm10/mm10.fasta PAIRED_RUN=false INCLUDE_SECONDARY_ALIGNMENTS=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
which generates the output:
[Mon Mar 06 13:23:14 EST 2017] Executing as con@gen on Linux 3.16.0-77-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_121-b00; Picard version: 1.138(89618e408692ff6288c7c880658f32f16fcbec53_1441135673) IntelDeflater
INFO 2017-03-06 13:23:14 SamAlignmentMerger [./aligned.sorted.bam]
[Mon Mar 06 13:23:14 EST 2017] picard.sam.MergeBamAlignment done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2022703104
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at picard.sam.AbstractAlignmentMerger.createNewCigarIfMapsOffEndOfReference(AbstractAlignmentMerger.java:631)
at picard.sam.AbstractAlignmentMerger.createNewCigarsIfMapsOffEndOfReference(AbstractAlignmentMerger.java:654)
at picard.sam.AbstractAlignmentMerger.updateCigarForTrimmedOrClippedBases(AbstractAlignmentMerger.java:686)
at picard.sam.AbstractAlignmentMerger.transferAlignmentInfoToFragment(AbstractAlignmentMerger.java:514)
at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:410)
at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:138)
at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:248)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
I asked this question GATK, but couldn't find a solution, and neither could the Drop-Seq group. I don't even understand what the underlying issue is.
As an aside, I've tried the latest version, but I get errors like this:
Unsupported major.minor version 52.0
The mesage is clear: