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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 #1597

Closed mszelest closed 4 months ago

mszelest commented 5 months ago

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)'

mizraelson commented 5 months ago

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

mszelest commented 5 months ago

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?

mizraelson commented 5 months ago

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?

mszelest commented 5 months ago

Hi,

Thank you for helping me with this issue. Below I attach a link with the fastq file.

Kind regards Monika CLL-0895_IGHV.fastq https://drive.google.com/file/d/1vv8IPXCADZnjC7vMmVx4JajUTisRXnfU/view?usp=drive_web

pon., 25 mar 2024 o 07:14 mizraelson @.***> napisał(a):

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?

— Reply to this email directly, view it on GitHub https://github.com/milaboratory/mixcr/issues/1597#issuecomment-2017300474, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFCP6WRKQKL6J72GM7UR63YZ66GHAVCNFSM6AAAAABFDKTUC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJXGMYDANBXGQ . You are receiving this because you authored the thread.Message ID: @.***>

bshim181 commented 5 months ago

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

mizraelson commented 5 months ago

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

2003100127 commented 5 months ago

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.

mizraelson commented 4 months ago

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.