NullPointerException during CollectGridssMetricsAndExtractSVReads

[vrohnie]

Dear All,

After some time of quite happliy using GRIDSS 2.5.10 within my pipeline, I wanted to update to the newest version...
However I get an Error for one of my "standard" test sets, which persists when using the official docker image of gridss 13.2.10.

I could probably share the data and the reference files of that would help to resolve the issue. It's WGS data from a yeast strain. I used bwa for mapping.

Please let me know if I can change something in the usage, which prevents this Error.

Best regards,
Veronika

Command:

docker run --rm -it -v /home:/home -w $PWD gridss/gridss:2.13.2 gridss --reference /home/micronap/Strains/CBS7435_Schaffer.fasta --output /home/micronap/AnalysisRuns/33852-20240819_0727/NG_12603_2_PD_F12/gridss/NG_12603_2_PD_F12_gridss_raw.vcf --assembly /home/micronap/AnalysisRuns/33852-20240819_0727/NG_12603_2_PD_F12/gridss/NG_12603_2_PD_F12_gridss_ass.bam --threads 4 /home/micronap/AnalysisRuns/33852-20240819_0727/NG_12603_2_PD_F12/NG_12603_2_PD_F12.dups_rem.bam

Error:

Mon Aug 19 08:01:37 UTC 2024: Running CollectGridssMetricsAndExtractSVReads|samtools /home/micronap/AnalysisRuns/33852-20240819_0727/NG_12603_2_PD_F12/NG_12603_2_PD_F12.dups_rem.bam
"$timecmd $samtools_sort -l 1 -n -T $tmp_prefix.namedsorted-tmp -Obam -o $tmp_prefix.namedsorted.bam /dev/stdin" command completed with exit code 1.

---

The underlying error message can be found in ./gridss.full.20240819_080124.c62ebcec5216.1.log

Detailed Error message:

********** The command line looks like this in the new syntax:

---

********** CollectGridssMetricsAndExtractSVReads -REFERENCE_SEQUENCE /home/micronap/Strains/CBS7435_Schaffer.fasta -TMP_DIR ./NG_12603_2_PD_F12.dups_rem.bam.gridss.working -ASSUME_SORTED true -I /home/micronap/AnalysisRuns/33852-20240819_0727/NG_12603_2_PD_F12/NG_12603_2_PD_F12.dups_rem.bam -O ./NG_12603_2_PD_F12.dups_rem.bam.gridss.working/NG_12603_2_PD_F12.dups_rem.bam -THRESHOLD_COVERAGE 50000 -FILE_EXTENSION null -GRIDSS_PROGRAM null -GRIDSS_PROGRAM CollectCigarMetrics -GRIDSS_PROGRAM CollectMapqMetrics -GRIDSS_PROGRAM CollectTagMetrics -GRIDSS_PROGRAM CollectIdsvMetrics -GRIDSS_PROGRAM ReportThresholdCoverage -PROGRAM null -PROGRAM CollectInsertSizeMetrics -SV_OUTPUT /dev/stdout -COMPRESSION_LEVEL 0 -INSERT_SIZE_METRICS ./NG_12603_2_PD_F12.dups_rem.bam.gridss.working/tmp.NG_12603_2_PD_F12.dups_rem.bam.insert_size_metrics -READ_PAIR_CONCORDANT_PERCENT 0.995 -UNMAPPED_READS false -MIN_CLIP_LENGTH 5 -INCLUDE_DUPLICATES true

---

08:00:18.735 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gridss/gridss-2.13.2-gridss-jar-with-dependencies.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Aug 19 08:00:18 UTC 2024] CollectGridssMetricsAndExtractSVReads MIN_CLIP_LENGTH=5 READ_PAIR_CONCORDANT_PERCENT=0.995 INSERT_SIZE_METRICS=./NG_12603_2_PD_F12.dups_rem.bam.gridss.working/tmp.NG_12603_2_PD_F12.dups_rem.bam.insert_size_metrics UNMAPPED_READS=false INCLUDE_DUPLICATES=true SV_OUTPUT=/dev/stdout GRIDSS_PROGRAM=[CollectCigarMetrics, CollectMapqMetrics, CollectTagMetrics, CollectIdsvMetrics, ReportThresholdCoverage] THRESHOLD_COVERAGE=50000 INPUT=/home/micronap/AnalysisRuns/33852-20240819_0727/NG_12603_2_PD_F12/NG_12603_2_PD_F12.dups_rem.bam ASSUME_SORTED=true OUTPUT=./NG_12603_2_PD_F12.dups_rem.bam.gridss.working/NG_12603_2_PD_F12.dups_rem.bam FILE_EXTENSION=null PROGRAM=[CollectInsertSizeMetrics] TMP_DIR=[./NG_12603_2_PD_F12.dups_rem.bam.gridss.working] COMPRESSION_LEVEL=0 REFERENCE_SEQUENCE=/home/micronap/Strains/CBS7435_Schaffer.fasta MIN_INDEL_SIZE=1 CLIPPED=true INDELS=true SPLIT=true SINGLE_MAPPED_PAIRED=true DISCORDANT_READ_PAIRS=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT 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
[Mon Aug 19 08:00:18 UTC 2024] Executing as root@f808330bb884 on Linux 6.1.0-18-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.13+8-Ubuntu-0ubuntu1.20.04; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.13.2-gridss
INFO 2024-08-19 08:00:18 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///dev/stdout
[Mon Aug 19 08:00:20 UTC 2024] gridss.CollectGridssMetricsAndExtractSVReads done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2149580800
Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Exception when running gridss.analysis.CollectIdsvMetrics
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:253)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:134)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:126)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:598)
at gridss.analysis.CollectGridssMetrics.doWork(CollectGridssMetrics.java:78)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:196)
at gridss.CollectGridssMetricsAndExtractSVReads.main(CollectGridssMetricsAndExtractSVReads.java:56)
Caused by: java.lang.RuntimeException: Exception when running gridss.analysis.CollectIdsvMetrics
at picard.analysis.SinglePassSamProgram.raiseAsyncException(SinglePassSamProgram.java:282)
at picard.analysis.SinglePassSamProgram.asyncAcceptRead(SinglePassSamProgram.java:273)
at picard.analysis.SinglePassSamProgram.asyncAcceptReads(SinglePassSamProgram.java:263)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:216)
... 7 more
Caused by: java.lang.NullPointerException
at htsjdk.samtools.SAMUtils.validateCigar(SAMUtils.java:937)
at htsjdk.samtools.SAMRecord.validateCigar(SAMRecord.java:1806)
at htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:284)
at htsjdk.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:607)
at htsjdk.samtools.SAMRecord.getUnclippedEnd(SAMRecord.java:632)
at gridss.analysis.CollectIdsvMetrics.acceptRead(CollectIdsvMetrics.java:53)
at picard.analysis.SinglePassSamProgram$SinglePassSamProgramRunner.run(SinglePassSamProgram.java:320)
at java.base/java.lang.Thread.run(Thread.java:829)
samtools sort: failed to read header from "/dev/stdin"