abra2 error java.lang.NumberFormatException

[rimzaag]

Once I try to run ABRA2, I get the following error. Would you please look into it? Thanks.

cmd=java -Xmx16G -jar target/abra2-2.19-jar-with-dependencies.jar --in /path_to/filesample_dedupSort.bam --out /path_to/filesample_abraRealign.bam --ref /path_to/hg19.fasta --threads 8 --targets /path_to/uploads_3091241_Covered-2.bed --tmpdir /path_to/tmpDir

INFO Fri Jan 18 10:34:36 CET 2019 Abra version: 2.19
INFO Fri Jan 18 10:34:36 CET 2019 Abra params: [/usr/local/bioinfo/Tools/abra2/target/abra2-2.19-jar-with-dependencies.jar --in /mnt/analyses/KDM-PROD/IOV_baseline/ResVarCall/IOV-KDM_N12enz/alignment/ALN_IOV_IOV_OKDM_IOV_N12enz_dedupSort.bam --out /mnt/analyses/KDM-PROD/IOV_baseline/ResVarCall/IOV-KDM_N12enz/alignment/ALN_IOV_IOV_OKDM_IOV_N12enz_20181012091021_abraRealign.bam --ref /mnt/analyses/Results/Reference/hg19.fasta --threads 8 --targets /mnt/analyses/PROJECT/kdm_IOV/uploads_3091241_Covered-ModifForAbraTest.bed --tmpdir /usr/local/bioinfo/Tools/abra2/tmpRim]
INFO Fri Jan 18 10:34:36 CET 2019 ABRA version: 2.19
INFO Fri Jan 18 10:34:36 CET 2019 input0: /mnt/analyses/KDM-PROD/IOV_baseline/ResVarCall/IOV-KDM_N12enz/alignment/ALN_IOV_IOV_OKDM_IOV_N12enz_dedupSort.bam
INFO Fri Jan 18 10:34:36 CET 2019 output0: /mnt/analyses/KDM-PROD/IOV_baseline/ResVarCall/IOV-KDM_N12enz/alignment/ALN_IOV_IOV_OKDM_IOV_N12enz_20181012091021_abraRealign.bam
INFO Fri Jan 18 10:34:36 CET 2019 regions: /mnt/analyses/PROJECT/kdm_IOV/uploads_3091241_Covered-ModifForAbraTest.bed
INFO Fri Jan 18 10:34:36 CET 2019 reference: /mnt/analyses/Results/Reference/hg19.fasta
INFO Fri Jan 18 10:34:36 CET 2019 num threads: 8
INFO Fri Jan 18 10:34:36 CET 2019 minEdgeFrequency: 0
minNodeFrequncy: 1
minContigLength: -1
minBaseQuality: 20
minReadCandidateFraction: 0.01
maxAverageRegionDepth: 1000
minEdgeRatio: 0.01

INFO Fri Jan 18 10:34:36 CET 2019 paired end: true
INFO Fri Jan 18 10:34:36 CET 2019 isSkipAssembly: false
INFO Fri Jan 18 10:34:36 CET 2019 useSoftClippedReads: true
INFO Fri Jan 18 10:34:36 CET 2019 SW scoring: [8, 32, 48, 1]
INFO Fri Jan 18 10:34:36 CET 2019 Soft clip params: [16, 13, 80, 15]
INFO Fri Jan 18 10:34:36 CET 2019 Java version: 1.8.0_191
INFO Fri Jan 18 10:34:36 CET 2019 hostname: bioit-dev
INFO Fri Jan 18 10:34:36 CET 2019 SG match,mismatch,gap_open_penalty,gap_extend_penalty: 8,-32,-48,-1
INFO Fri Jan 18 10:34:36 CET 2019 Using temp directory: /usr/local/bioinfo/Tools/abra2/tmpRim/abra2_358def45-c903-44a8-a674-5bc2c317367f1665716855282894176
INFO Fri Jan 18 10:34:36 CET 2019 Loading native library from: /usr/local/bioinfo/Tools/abra2/tmpRim/abra2_358def45-c903-44a8-a674-5bc2c317367f1665716855282894176/libAbra.so
INFO Fri Jan 18 10:34:36 CET 2019 Loading reference map: /mnt/analyses/Results/Reference/hg19.fasta
INFO Fri Jan 18 10:36:10 CET 2019 Done loading ref map. Elapsed secs: 93
INFO Fri Jan 18 10:36:10 CET 2019 Reading Input SAM Header and identifying read length
INFO Fri Jan 18 10:36:10 CET 2019 Identifying header and determining read length
INFO Fri Jan 18 10:36:13 CET 2019 Min insert length: 0
INFO Fri Jan 18 10:36:13 CET 2019 Max insert length: 230110226
INFO Fri Jan 18 10:36:13 CET 2019 Max read length is: 150
INFO Fri Jan 18 10:36:13 CET 2019 Min contig length: 151
INFO Fri Jan 18 10:36:13 CET 2019 Read length: 150
INFO Fri Jan 18 10:36:13 CET 2019 Loading target regions
INFO Fri Jan 18 10:36:13 CET 2019 Loading target regions from : /mnt/analyses/PROJECT/kdm_IOV/uploads_3091241_Covered-ModifForAbraTest.bed
INFO Fri Jan 18 10:36:13 CET 2019 Collapsed regions from 1160 to 1029
INFO Fri Jan 18 10:36:13 CET 2019 Num regions: 1300
INFO Fri Jan 18 10:36:13 CET 2019 Total junctions input: 0
INFO Fri Jan 18 10:36:13 CET 2019 Final Junctions: 0, Variant Junctions: 0
INFO Fri Jan 18 10:36:13 CET 2019 Intel deflater disabled
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_1_25000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_25000001_50000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_50000001_75000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_75000001_100000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_100000001_125000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_125000001_150000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_175000001_200000000
INFO Fri Jan 18 10:36:13 CET 2019 Processing chromosome chunk: chr1_150000001_175000000
java.lang.NumberFormatException: For input string: "-3,265707"
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 abra.ScoredContig.convertAndFilter(ScoredContig.java:53)
at abra.ReAligner.assemble(ReAligner.java:1114)
at abra.ReAligner.processRegion(ReAligner.java:1293)
at abra.ReAligner.processChromosomeChunk(ReAligner.java:361)
at abra.ReAlignerRunnable.go(ReAlignerRunnable.java:21)
at abra.AbraRunnable.run(AbraRunnable.java:20)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

[mozack]

There is an issue with commas being used as the decimal place with your locale. I will address this in the software in a future release.

As a workaround, please set your locale to en_US.UTF-8 when running ABRA2. i.e.

export LC_ALL=en_US.UTF-8

You can reset to the original value afterwards using:

export LC_ALL=fr_BE.UTF-8

[sybrohee]

Great ... solved my issue (abra 2.23)

[your-highness]

Kudos! It's still an issue in abra-2.23

[Islanov-Igor]

Abra-2.24
Still an issue. Had to put the workaround in the pipeline.