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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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virus breakend error #565

Open shashank-bgp opened 2 years ago

shashank-bgp commented 2 years ago

I am getting following error:

Thu Feb 17 07:53:17 UTC 2022: Identifying viral sequences Thu Feb 17 07:53:18 UTC 2022: Treating 0 reference sequences as viral sequences. Thu Feb 17 07:53:58 UTC 2022: Identifying viral taxa in sample based on kraken2 summary report Thu Feb 17 07:54:08 UTC 2022: Exit status 0 for $timecmd java -Xmx8g $jvm_args -cp $gridss_jar gridss.kraken.IdentifyViralTaxa --INPUT_KRAKEN2_REPORT $file_report --OUTPUT $file_summary_taxa_tsv --REPORT_OUTPUT $file_viral_report --SUMMARY_REPORT_OUTPUT $file_extracted_report --NCBI_NODES_DMP $nodesdmp --SEQID2TAXID_MAP $seqidtaxidmap --MIN_SUPPORTING_READS $minreads --TAXONOMIC_DEDUPLICATION_LEVEL Genus $taxid_args 1>&2 2>> $logfile

See log file ./SRR5090597.virusbreakend.vcf.virusbreakend.working/virusbreakend.20220217_075317.ip-172-21-10-139.4572.log for underlying error

Runtime.totalMemory()=2405433344 Exception in thread "main" java.lang.NullPointerException at gridss.kraken.IdentifyViralTaxa.createSummaryLine(IdentifyViralTaxa.java:182) at gridss.kraken.IdentifyViralTaxa.lambda$doWork$11(IdentifyViralTaxa.java:153) at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195) at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1654) at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474) at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913) at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578) at gridss.kraken.IdentifyViralTaxa.doWork(IdentifyViralTaxa.java:154) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305) at gridss.kraken.IdentifyViralTaxa.main(IdentifyViralTaxa.java:221)

Please help me rectify the error.

alexjfortuna commented 2 years ago

I am having the same issue. Did you ever have any luck?