Open rimzaag opened 5 years ago
mozack
commented
5 years ago 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
commented
4 years ago Great ... solved my issue (abra 2.23)
your-highness
commented
3 years ago Kudos! It's still an issue in abra-2.23
Islanov-Igor
commented
6 months ago Abra-2.24 Still an issue. Had to put the workaround in the pipeline.
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)