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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Exception in thread "main" java.lang.NullPointerException #234

Closed joe-jhou2 closed 7 years ago

joe-jhou2 commented 7 years ago

java version "1.8.0_121" java(TM) SE Runtime Environment (build 1.8.0_121-b13) java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

F:\MUX4446\2017_01_13_15_38_00_981\RMM592>java -Xmx4g -Xms3g -jar C:\Users\jhou Downloads\mixcr-2.1.1\mixcr.jar align -s mmu -r alignmentReport_RMM592.txt RMM59 2_MS001-PE-R00400_L001_R1.fastq.gz RMM592_MS001-PE-R00400_L001_R2.fastq.gz align ments_RMM592.vdjca Reference library: repseqio.v1.2:10090 (9a1b61eb20896bbb44a5d38d9359107b) WARNING: Functional gene IGKV8-23-1*00 doesn't contain full VRegionWithP (exclud ed) WARNING: ... 7 more functional genes excluded due to absent "featureToAlign". Alignment: 0.1% Alignment: 9.4% ETA: 00:19:31 Exception in thread "main" java.lang.NullPointerException at com.milaboratory.mixcr.vdjaligners.VDJCAlignerPVFirst.process0(VDJCAl ignerPVFirst.java:97) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerPVFirst.process0(VDJCAl ignerPVFirst.java:55) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.ja va:74) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJC AlignerWithMerge.java:86) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJC AlignerWithMerge.java:42) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.ja va:74) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.ja va:44) at cc.redberry.pipe.CUtils$9.process(CUtils.java:350) at cc.redberry.pipe.CUtils$9.process(CUtils.java:345) at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcesso r.java:304) at java.lang.Thread.run(Unknown Source)

joe-jhou2 commented 7 years ago

I use another Mac computer to run the same sample and code, with the same error info as below: mixcr align -s mmu -r alignmentReport_RMM590.txt RMM590_MS001-PE-R00400_L001_R1.fastq.gz RMM590_MS001-PE-R00400_L001_R2.fastq.gz alignments_RMM590.vdjca Reference library: repseqio.v1.2:10090 (9a1b61eb20896bbb44a5d38d9359107b) WARNING: Functional gene IGKV8-23-1*00 doesn't contain full VRegionWithP (excluded) WARNING: ... 7 more functional genes excluded due to absent "featureToAlign". Alignment: 0.1% Alignment: 4.8% ETA: 00:40:02 Alignment: 10.4% ETA: 00:32:00 Alignment: 15.7% ETA: 00:31:50 Alignment: 21.4% ETA: 00:27:45 Alignment: 27.2% ETA: 00:25:05 Alignment: 33.1% ETA: 00:23:04 Alignment: 38.8% ETA: 00:21:28 Alignment: 44.7% ETA: 00:18:47 Alignment: 50.4% ETA: 00:17:17 Alignment: 56.3% ETA: 00:15:01 Alignment: 62.1% ETA: 00:13:06 Alignment: 67.1% ETA: 00:13:16 Exception in thread "main" java.lang.NullPointerException at com.milaboratory.mixcr.vdjaligners.VDJCAlignerPVFirst.process0(VDJCAlignerPVFirst.java:97) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerPVFirst.process0(VDJCAlignerPVFirst.java:55) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:74) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJCAlignerWithMerge.java:86) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJCAlignerWithMerge.java:42) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:74) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:44) at cc.redberry.pipe.CUtils$9.process(CUtils.java:350) at cc.redberry.pipe.CUtils$9.process(CUtils.java:345) at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:304) at java.lang.Thread.run(Thread.java:745)

MiXCR v2.1.1 (built Thu Mar 02 14:03:41 PST 2017; rev=9cbb23c; branch=release/v2.1.1) RepSeq.IO v1.2.7 (rev=a06d5b2) MiLib v1.7.2 (rev=4a8aaf6) Built-in V/D/J/C library: repseqio.v1.2

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dbolotin commented 7 years ago

Thanks for reporting! Can you share this dataset? The problem seems to be tricky, and having the data to reproduce it would really speed-up the debugging process. We will of course keep it confidential and remove it after resolution of the bug. If it is possible please write me to bolotin.dmitriy@gmail.com.