Closed rimzaag closed 5 years ago
mozack
commented
5 years ago Please log abra2 issues with the abra2 project:
https://github.com/mozack/abra2
Can you please send me the locale for the machine on which you are running abra2? i.e. Run the locale command on the command line and send the output.
rimzaag
commented
5 years ago Thank you for your reply output for locale command
locale LANG=fr_BE.UTF-8 LANGUAGE=fr_BE:fr LC_CTYPE="fr_BE.UTF-8" LC_NUMERIC="fr_BE.UTF-8" LC_TIME="fr_BE.UTF-8" LC_COLLATE="fr_BE.UTF-8" LC_MONETARY="fr_BE.UTF-8" LC_MESSAGES="fr_BE.UTF-8" LC_PAPER="fr_BE.UTF-8" LC_NAME="fr_BE.UTF-8" LC_ADDRESS="fr_BE.UTF-8" LC_TELEPHONE="fr_BE.UTF-8" LC_MEASUREMENT="fr_BE.UTF-8" LC_IDENTIFICATION="fr_BE.UTF-8" LC_ALL=
knowing for java i work with java 8
java -version openjdk version "1.8.0_191" OpenJDK Runtime Environment (build 1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12) OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode)
mozack
commented
5 years ago This issue is transferred to: https://github.com/mozack/abra2/issues/25
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)