ucagenomix/sicelore

Sicelore-2.0.jar ComputeConsensus exception in LongreadParser

jbeaulaurier opened this issue · 1 comments

jbeaulaurier commented

Any help in decoding this exception would be greatly appreciated. Permissions to the temp directory should not be an issue and I have the following executables in my PATH:

  • spoa
  • picard
  • samtools
  • minimap2
  • racon

If I revert back to Sicelore-1.0.jar, I'm able to produce a consensus FASTA file.

Command

java -jar -Xmx22g ~/projects_new/software/sicelore/Jar/Sicelore-2.0.jar ComputeConsensus I=8-ont_merge/hsmm.GEUS10xAttributes_umifound_.bam O=hsmm.molecules.fastq T=4 TMPDIR=/home/temp/

Output

[Wed Aug 04 00:02:38 BST 2021] ComputeConsensus INPUT=8-ont_merge/hsmm.GEUS10xAttributes_umifound_.bam OUTPUT=hsmm.molecules.fastq NTHREADS=4 TMPDIR=/home/temp/ CELLTAG=BC UMITAG=U8 GENETAG=IG TSOENDTAG=TE UMIENDTAG=UE POLYAENDTAG=PE USTAG=US RNTAG=RN MAXCLIP=150 MAPQV0=false MAXREADS=20 MINPS=3 MAXPS=20 DEBUG=false 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
[Wed Aug 04 00:02:38 BST 2021] Executing as jbeaulaurier@porpoisehead00 on Linux 4.4.0-142-generic amd64; OpenJDK 64-Bit Server VM 11.0.9.1-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: null
INFO 2021-08-04 00:02:38 LongreadParser start...

java.lang.NullPointerException
at org.ipmc.sicelore.utils.LongreadRecord.fromSAMRecord(LongreadRecord.java:91)
at org.ipmc.sicelore.utils.LongreadParser.parseSAMRecord(LongreadParser.java:100)
at org.ipmc.sicelore.utils.LongreadParser.(LongreadParser.java:62)
at org.ipmc.sicelore.programs.ComputeConsensus.doWork(ComputeConsensus.java:100)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:277)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at org.ipmc.sicelore.cmdline.SiCeLoReMain.main(SiCeLoReMain.java:40)

INFO 2021-08-04 00:02:38 LongreadParser end...
INFO 2021-08-04 00:02:38 LongreadParser Total SAMrecords 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords valid 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords unvalid 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords mapqv=0 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords no gene 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords no UMI 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords chimeria 0
INFO 2021-08-04 00:02:38 LongreadParser SAMrecords reversed 0
INFO 2021-08-04 00:02:38 LongreadParser Total reads 0
INFO 2021-08-04 00:02:38 LongreadParser Total reads multiSAM 0
INFO 2021-08-04 00:02:38 MoleculeDataset MoleculeDataset init start...
INFO 2021-08-04 00:02:38 MoleculeDataset Total molecules 0
INFO 2021-08-04 00:02:38 MoleculeDataset Total molecule reads 0
INFO 2021-08-04 00:02:38 MoleculeDataset Total molecule multiIG 0
INFO 2021-08-04 00:02:38 MoleculeDataset Calling consensus start with 4 threads
INFO 2021-08-04 00:02:38 MoleculeDataset Total consensus to compute 0
[Wed Aug 04 00:02:38 BST 2021] org.ipmc.sicelore.programs.ComputeConsensus done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2147483648

jbeaulaurier commented

Closing this because a new git pull solved the problem for me.