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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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no report file in mixcr align with error like exception in thread "main" java.lang.IllegalStateException: TotalReads count not set. #183

Closed haoecust closed 7 years ago

haoecust commented 7 years ago

I used the command "mixcr-2.0.2/mixcr align --report sample_align.log --species mmu --threads 18 sample.R1.fastq sample.R2.fastq sample.vdjca ".

sample.vdjca was successfully generated. However, "sample_align.log" is failed with an error like "exception in thread "main" java.lang.IllegalStateException: TotalReads count not set."

Would you please help to figure out what's wrong with it.

Thanks.

dbolotin commented 7 years ago

Please post full stack-trace here.

dbolotin commented 7 years ago

And also commands to reproduce the problem.

haoecust commented 7 years ago

@dbolotin I just found that the vdjca file may be not completely generated. The details of commands and errors were listed as following.

[haoecust@OncServer test_data]$ /program/mixcr-2.0.2/mixcr align --report test_align.log --species mmu --threads 8 test_TRB_CDR3.R1.fastq test_TRB_CDR3.R2.fastq ./test_TRB/test_TRB_CDR3.vdjca

Reference library: repseqio.v1.1:10090 (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% Alignment: 10% ETA: 00:06:08 Alignment: 20.2% ETA: 00:05:15 Alignment: 30.2% ETA: 00:04:36 Alignment: 40.3% ETA: 00:03:56 Alignment: 50.6% ETA: 00:03:17 Alignment: 60.7% ETA: 00:02:43 Alignment: 70.8% ETA: 00:01:59 Alignment: 81% ETA: 00:01:18 Alignment: 91.1% ETA: 00:00:36 Exception in thread "main" com.milaboratory.core.io.sequence.IllegalFileFormatException at com.milaboratory.core.io.sequence.fastq.FastqRecordsReader.nextRecord(FastqRecordsReader.java:160) at com.milaboratory.core.io.sequence.fastq.SingleFastqReader.take(SingleFastqReader.java:299) at com.milaboratory.core.io.sequence.fastq.SingleFastqReader.take(SingleFastqReader.java:35) at com.milaboratory.core.io.sequence.AbstractMultiReader.takeReads(AbstractMultiReader.java:52) at com.milaboratory.core.io.sequence.PairedReader.take(PairedReader.java:28) at com.milaboratory.core.io.sequence.PairedReader.take(PairedReader.java:21) at cc.redberry.pipe.util.Chunk.readChunk(Chunk.java:55) at cc.redberry.pipe.CUtils$7.take(CUtils.java:323) at cc.redberry.pipe.CUtils$7.take(CUtils.java:315) at cc.redberry.pipe.blocks.O2ITransmitter.run(O2ITransmitter.java:66) at java.lang.Thread.run(Thread.java:745)

haoecust commented 7 years ago

@dbolotin Very strange. I test another testing sample from the same sequencing platform. It seems the results were well generated.

[haoecust@OncServer test_data]$ /program/mixcr-2.0.2/mixcr align --report test2_align.log --species mmu --threads 8 test2.R1.fastq test2.R2.fastq ./test_TRB/test2_CDR3.vdjca

Reference library: repseqio.v1.1:10090 (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% Alignment: 10.2% ETA: 00:05:44 Alignment: 20.2% ETA: 00:04:54 Alignment: 30.5% ETA: 00:04:18 Alignment: 40.5% ETA: 00:03:38 Alignment: 50.8% ETA: 00:03:02 Alignment: 60.9% ETA: 00:02:30 Alignment: 71% ETA: 00:01:49 Alignment: 81.2% ETA: 00:01:11 Alignment: 91.2% ETA: 00:00:33 ============= Report ============== Analysis time: 6.30m Total sequencing reads: 2620365 Successfully aligned reads: 2438296 (93.05%) Alignment failed, no hits (not TCR/IG?): 18295 (0.7%) Alignment failed because of absence of J hits: 160176 (6.11%) Alignment failed because of low total score: 3598 (0.14%) Overlapped: 2349012 (89.64%) Overlapped and aligned: 2198372 (83.9%) Overlapped and not aligned: 150640 (5.75%) [TRA] chains: 6801 (0.28%) [TRB] chains: 2431484 (99.72%) [TRD] chains: 3 (0%) [IGL] chains: 8 (0%)

haoecust commented 7 years ago

@dbolotin Thank you. I think I have figure it out. The test data is partially missing during the downloading process. I re-downloaded the test data, currently, all of them are smoothly runing.

Have a nice holiday!