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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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Generic-ont alignment problem

mszelest opened this issue · comments

commented

I've tried to use my ONT data (I used SQK-LSK109 kit for IGHV sequencing) to analyze data but alignment stops at some point and I don't understand whats wrong?

'mixcr align --report CLL-0895_result.align.report.txt --json-report CLL-0895_result.align.report.json --preset generic-ont --save-output-file-names CLL-0895_result.align.list --dna --species hsa CLL-0895_IGHV.fastq CLL-0895_result.vdjca'

'Running:
mixcr align --report CLL-0895_result.align.report.txt --json-report CLL-0895_result.align.report.json --preset generic-ont --save-output-file-names CLL-0895_result.align.list --dna --species hsa CLL-0895_IGHV.fastq CLL-0895_result.vdjca
Alignment: 0%
Alignment: 3,7% ETA: 00:52:17
Alignment: 6,1% ETA: 01:18:15
Alignment: 8,5% ETA: 01:15:53
Alignment: 11,4% ETA: 01:01:13
Alignment: 14,3% ETA: 00:59:36
Alignment: 17,5% ETA: 00:51:17
Alignment: 20,6% ETA: 00:52:17
Alignment: 23,3% ETA: 00:56:35
Alignment: 26,1% ETA: 00:54:18
Alignment: 28,9% ETA: 00:49:15
Alignment: 32,6% ETA: 00:36:43
Alignment: 35,4% ETA: 00:47:36
Alignment: 38,1% ETA: 00:45:22
Alignment: 40,7% ETA: 00:46:16
Alignment: 44,2% ETA: 00:31:45
Alignment: 47,4% ETA: 00:32:52
Alignment: 51,1% ETA: 00:26:36
Alignment: 54% ETA: 00:31:57
java.lang.AssertionError
at com.milaboratory.o.bM.a(SourceFile:95)
at com.milaboratory.o.aX.c(SourceFile:3067)
at com.milaboratory.o.aX.e(SourceFile:99)
at com.milaboratory.o.aS.c(SourceFile:41)
at com.milaboratory.mixcr.cli.CommandAlignPipeline$ProcessingBundle.(SourceFile:464)
at com.milaboratory.mixcr.cli.CommandAlign$Cmd$createReader$4.invoke(SourceFile:995)
at com.milaboratory.mixcr.cli.CommandAlign$Cmd$createReader$4.invoke(SourceFile:995)
at com.milaboratory.o.EO.process(SourceFile:31)
at cc.redberry.pipe.util.SimpleProcessorWrapper.take(SimpleProcessorWrapper.java:43)
at com.milaboratory.o.ER.take(SourceFile)
at cc.redberry.pipe.util.Chunk.readChunk(Chunk.java:78)
at cc.redberry.pipe.CUtils$2.take(CUtils.java:169)
at cc.redberry.pipe.CUtils$2.take(CUtils.java:161)
at cc.redberry.pipe.blocks.O2ITransmitter.run(O2ITransmitter.java:63)
at java.base/java.lang.Thread.run(Thread.java:832)'

commented

Hi, can you please try the latest MiXCR version and let me know if the issue is still there.

commented

Thanks for a quick response! I got this version:
App version: 4.6.0; built=Sat Dec 09 20:48:42 CET 2023; rev=c9fafa41fe; lib=repseqio.v4.0
Isn't it the latest version?

commented

Yes, 4.6 is the latest version so far. It seems the issue lies with the FASTQ quality parsing. Would it be possible for you to share the problematic file?

commented
commented

I am facing the same issue and I was wondering if it has been resolved yet.

commented

Hi,
So, the issue is with an unexpectedly long read length. We will fix it and I will reply with a updated version soon.

commented

Hi, So, the issue is with an unexpectedly long read length. We will fix it and I will reply with a updated version soon.

Thanks, please. I am having the same issue and waiting for your feedback. Or if there is a version to fall back.

commented

Hi, we have added a fix in the latest develop version. Please try and let me know if it works. I will close this issue for now. Feel free to reopen if needed.