unknown error using ConvertTagToReadGroup
Closed this issue · 2 comments
Hi,
I have tried to run ConvertTagToReadGroup on my dataset. The job seems failed but I do not know what happened. Could you advise me on how to fix it?
Thanks,
Cynthia
********** The command line looks like this in the new syntax:
********** ConvertTagToReadGroup -I donor12_markdup_sorted.bam -O donor12added -CELL_BARCODE_TAG XC -CELL_BC_FILE filtered100K_donor12.txt -SAMPLE_NAME donor12
21:00:39.546 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/mcfiles/cliu/Drop-seq_tools-2.4.0/jar/lib/picard-2.20.5.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue May 04 21:00:39 AEST 2021] ConvertTagToReadGroup INPUT=donor12_markdup_sorted.bam OUTPUT=donor12added CELL_BARCODE_TAG=XC CELL_BC_FILE=filtered100K_donor12.txt SAMPLE_NAME=donor12 READ_MQ=10 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
[Tue May 04 21:00:39 AEST 2021] Executing as cliu@scn02.svi.edu.au on Linux 3.10.0-1160.15.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_282-b08; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.4.0(3d2b3d8_1600201514)
[Tue May 04 21:00:39 AEST 2021] org.broadinstitute.dropseqrna.utils.ConvertTagToReadGroup done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2058354688
Exception in thread "main" java.lang.NullPointerException
at org.broadinstitute.dropseqrna.utils.ConvertTagToReadGroup.getReadGroupTemplate(ConvertTagToReadGroup.java:145)
at org.broadinstitute.dropseqrna.utils.ConvertTagToReadGroup.doWork(ConvertTagToReadGroup.java:92)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at org.broadinstitute.dropseqrna.cmdline.DropSeqMain.main(DropSeqMain.java:42)
It's been a while since we heard from you, I hope the last comment fixed your issue.