TagReadWithGeneFunction v2.3.0, java.lang.NullPointerException
MonkeySylvia opened this issue · comments
Hi,
I want to tag my aligned bam file with the gene tag by "TagReadWithGeneFunction", but I can't get it running. I can't figure out why either. My "TagReadWithGeneFunction " version is v2.3.0. Thank you in advance for helping!
Here is my bam
NB501337:174:HCCKHBGX2:3:22610:11803:1662 16 chr1 1323 6 62M * 0 0 TTCTCTATTGTTTTGACCTTCAGCAGTGAAAATTAAACACTGAAATTAATCTCTGAAAACTG //<////</A/////EEE//E<<E6///AA/////6/EAE//E////<//A///E<//AA/6 XC:Z:CAGATGTGGCCA MD:Z:4T0C34C21 PG:Z:bowtie2 RG:Z:A NM:i:3 XM:Z:GGGGAAGC UQ:i:42 AS:i:-9
NB501337:174:HCCKHBGX2:1:11305:16993:3443 16 chr1 1325 1 54M * 0 0 CTTTATTGTTTTGACCTTCAGCAGTGAAAATTAAACACTGAAATTAATCTCTGA /EEEAE<<EEEAAEEEEE6EEEEEEAAEEEEAAEE/E//EEEEEEEEEEAAAAA XC:Z:CAGATGTGGCCA MD:Z:3C34C15 PG:Z:bowtie2 RG:Z:A NM:i:2 XM:Z:GGGGAAGC UQ:i:50 AS:i:-8
NB501337:174:HCCKHBGX2:2:23306:15475:8140 16 chr1 1325 6 49M * 0 0 CTTTATTGTTTTGACCTTCAGCAGTGAAAATTAAACACTGAAATTAATC EEE<EEEAEEEAEEEEAEEEEAEEEAEEEEEEEEEEEEEEEEEAA<AAA XC:Z:CAGATGTGGCCA MD:Z:3C34C10 PG:Z:bowtie2 RG:Z:A NM:i:2 XM:Z:GGGGAAGC UQ:i:63 AS:i:-9
here is my code
Drop-seq_tools-2.3.0/TagReadWithGeneFunction INPUT=ZF30-DS5.realigned.barcoded.bam OUTPUT=ZF30-DS5.realigned.genebarcoded.bam GENE_FUNCTION_TAG=null READ_FUNCTION_TAG=null ANNOTATIONS_FILE=danRer11.gene.nonoverlapte.1123.refFlat &
and my error message
`23:09:27.733 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/local/workdir/nc499/tools/Drop-seq_tools-2.3.0/jar/lib/picard-2.18.14.jar!/com/intel/gkl/native/libgkl_compression.so
23:09:27.742 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
23:09:27.743 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/local/workdir/nc499/tools/Drop-seq_tools-2.3.0/jar/lib/picard-2.18.14.jar!/com/intel/gkl/native/libgkl_compression.so
23:09:27.744 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (No such file or directory)
TagReadWithGeneFunction INPUT=ZF30-DS5.bam OUTPUT=test.bam GENE_FUNCTION_TAG=null READ_FUNCTION_TAG=null ANNOTATIONS_FILE=danRer11.gene.nonoverlapte.1123.refFlat GENE_NAME_TAG=gn GENE_STRAND_TAG=gs USE_STRAND_INFO=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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Sun Nov 24 23:09:27 EST 2019] Executing as xxxxx on Linux 3.10.0-957.10.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_212-b04; Deflater: Jdk; Inflater: Jdk; Provider GCS is not available; Picard version: 2.3.0(34e6572_1555443285)
23:09:27.784 WARN IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
23:09:28.323 WARN IntelDeflaterFactory - IntelDeflater is not supported, using Java.util.zip.Deflater
[Sun Nov 24 23:09:28 EST 2019] org.broadinstitute.dropseqrna.metrics.TagReadWithGeneFunction done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2058354688
Exception in thread "main" java.lang.NullPointerException
at htsjdk.samtools.SAMTagUtil.makeBinaryTag(SAMTagUtil.java:100)
at htsjdk.samtools.SAMRecord.setAttribute(SAMRecord.java:1425)
at org.broadinstitute.dropseqrna.metrics.TagReadWithGeneFunction.setAnnotations(TagReadWithGeneFunction.java:205)
at org.broadinstitute.dropseqrna.metrics.TagReadWithGeneFunction.doWork(TagReadWithGeneFunction.java:121)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at org.broadinstitute.dropseqrna.cmdline.DropSeqMain.main(DropSeqMain.java:42)
`
Hi @MonkeySylvia ,
This problem is cause by this command-line argument:
GENE_FUNCTION_TAG=null
This program assigns a value to whatever GENE_FUNCTION_TAG you specify. It doesn't make sense to set GENE_FUNCTION_TAG to null.
Regards, Alec
That fixed the issue, thank you Alec!
Sylvia