GRIDSS exiting without providing output

[MaestSi]

Hi,
I am running GRIDSS v2.6.2 with command:

GRIDSS=/mnt/cifs01/simone/software/gridss/scripts/gridss.sh
WORKING_DIR=/mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST
REFERENCE=$WORKING_DIR/Homo_sapiens_assembly38.fasta
BAM=$WORKING_DIR/NA24385_30X.bam

$GRIDSS \
--reference $REFERENCE \
--output $WORKING_DIR/GRIDSS_output.vcf.gz \
--assembly $WORKING_DIR/NA24385_assembly.bam \
--threads 24 \
--jar /mnt/cifs01/simone/software/gridss/gridss-2.6.2-gridss-jar-with-dependencies.jar \
--workingdir $WORKING_DIR \
$BAM

Stdout is the following:

Using working directory "/mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST"
Using reference genome "/mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/Homo_sapiens_assembly38.fasta"
Using assembly bam /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/NA24386_assembly.bam
Using output VCF /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/GRIDSS_output.vcf.gz
WARNING: GRIDSS scales sub-linearly at high thread count. Up to 8 threads is the recommended level of parallelism.
Using 24 worker threads.
Using no blacklist bed. The encode DAC blacklist is recommended for hg19.
Using JVM maximum heap size of 25g for assembly and variant calling.
Using input file /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/NA24385_30X.bam
Found /mnt/cifs01/simone/software/miniconda3/envs/GRIDSS_env/bin/bwa
Found /mnt/cifs01/simone/software/miniconda3/envs/GRIDSS_env/bin/Rscript
Found /usr/bin/time
Found /mnt/cifs01/simone/software/miniconda3/envs/GRIDSS_env/bin/sambamba
Found /mnt/cifs01/simone/software/miniconda3/envs/GRIDSS_env/bin/java
sambamba 0.7.0
R scripting front-end version 3.6.1 (2019-07-05)
bwa Version: 0.7.17-r1188
GNU time 1.7
GNU bash, version 4.3.11(1)-release (x86_64-pc-linux-gnu)
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)
Max file handles: 16384
dom 29 set 2019, 19.49.37, CEST Running GRIDSS. The full log is in /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/gridss.full.20190929_194937.hiseq2.11457.log
dom 29 set 2019, 19.49.37, CEST Start pre-processing /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/NA24385_30X.bam
dom 29 set 2019, 19.49.37, CEST CollectInsertSizeMetrics /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/NA24385_30X.bam first 10000000 records
dom 29 set 2019, 19.50.30, CEST CollectGridssMetricsAndExtractSVReads|sambamba /mnt/cifs01/simone/NA24385/30X/GRIDSS_TEST/NA24385_30X.bam
"/usr/bin/time -a -o $timinglogfile sambamba sort -n --tmpdir $dir -m 8GB -o $tmp_prefix.namedsorted.bam -t $threads /dev/stdin" command completed with exit code 1.

The last lines in the log file are the followings:

Exception in thread "main" java.lang.NumberFormatException: For input string: "567,176827"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at htsjdk.samtools.util.FormatUtil.parseDouble(FormatUtil.java:141)
at htsjdk.samtools.util.FormatUtil.parseObject(FormatUtil.java:191)
at htsjdk.samtools.metrics.MetricsFile.read(MetricsFile.java:388)
at gridss.analysis.InsertSizeDistribution.create(InsertSizeDistribution.java:33)
at gridss.cmdline.ProcessStructuralVariantReadsCommandLineProgram.getReadPairConcordanceCalculator(ProcessStructuralVariantReadsCommandLineProgram.java:68)
at gridss.analysis.CollectStructuralVariantReadMetrics.setup(CollectStructuralVariantReadMetrics.java:51)
at gridss.ExtractSVReads.setup(ExtractSVReads.java:50)
at gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram.setup(ByReadNameSinglePassSamProgram.java:156)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:138)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:563)
at gridss.analysis.CollectGridssMetrics.doWork(CollectGridssMetrics.java:66)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:190)
at gridss.CollectGridssMetricsAndExtractSVReads.main(CollectGridssMetricsAndExtractSVReads.java:61)
sambamba-sort: not enough data in stream

Do you have any advice about how to solve this error?
Thanks in advance,
Simone

[d-cameron]

The issue is that numbers are getting written with a comma separator, yet expecting a peroid in the next step.

Do you have any advice about how to solve this error?

Run

export LC_ALL=C

before running GRIDSS to force a consistent locale.

gridss.sh will include this fix in the script itself in the next release.

Thanks for the bug report.

[MaestSi]

Thank you!

[YuanwenGuo]

Hello,
I got similar error log file during SV calling process, even after adding export LC_ALL=C. Just wonder if this issue has been fixed and how to make it work?

Please see my error log records as following:
gridss.SoftClipsToSplitReads done. Elapsed time: 470.26 minutes.
Runtime.totalMemory()=4151836672
Exception in thread "main" java.lang.NumberFormatException: For input string: "asm4-34583"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at au.edu.wehi.idsv.SplitReadHelper.getRealignmentFirstAlignedBaseReadOffset(SplitReadHelper.java:231)
at au.edu.wehi.idsv.SplitReadHelper.unclip(SplitReadHelper.java:175)
at au.edu.wehi.idsv.SplitReadHelper.replaceAlignment(SplitReadHelper.java:275)
at au.edu.wehi.idsv.SplitReadHelper.replaceAlignment(SplitReadHelper.java:260)
at au.edu.wehi.idsv.SplitReadRealigner.prepareRecordsForWriting(SplitReadRealigner.java:273)
at au.edu.wehi.idsv.SplitReadRealigner.writeCompletedAlignment(SplitReadRealigner.java:237)
at au.edu.wehi.idsv.SplitReadRealigner.mergeSupplementaryAlignment(SplitReadRealigner.java:384)
at au.edu.wehi.idsv.SplitReadRealigner.mergeSupplementaryAlignment(SplitReadRealigner.java:340)
at au.edu.wehi.idsv.SplitReadRealigner.createSupplementaryAlignments(SplitReadRealigner.java:310)
at gridss.SoftClipsToSplitReads.doWork(SoftClipsToSplitReads.java:95)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at gridss.SoftClipsToSplitReads.main(SoftClipsToSplitReads.java:118)
INFO 2019-10-10 17:34:34 IdentifyVariants

Much appreciate if anyone can help with this issue.

Best,
Yuanwen