assembleContigs doesn't progress

[ericavalentini]

Checklist before submitting the issue:

• The issue is strongly related to the MiXCR software
• The issue can be reproduced with the most recent version of MiXCR (I'm using the development version to be able to use 10x-sc-xcr-vdj-gemx-v3)
• There is no answer to the question in the official documentation and there is no duplicate issue in the bug tracker
• Inspection of raw alignments with exportAlignmentsPretty shows that data has the expected architecture, and sample preparation artefacts are not the reason of the problem (if this is the matter of the issue)

Expected Result

The command

mixcr -Xmx100g analyze 10x-sc-xcr-vdj-gemx-v3 \
  --species mouse \
  --force-overwrite \
  --use-local-temp \
  -t 24 \
  data/AS-1877659-LR-83642_S1_R1_001.fastq.gz \
  data/AS-1877659-LR-83642_S1_R2_001.fastq.gz \
  result/AS-1877659-LR-83642_result

should progress until the end

Actual Result

The command is stuck at the following step:

Running:
mixcr assembleContigs -f --report result/AS-1877659-LR-83642_result.assembleContigs.report.txt --json-report result/AS-1877659-LR-83642_result.assembleContigs.report.json --threads 24 result/AS-1877659-LR-83642_result.clna result/AS-1877659-LR-83642_result.contigs.clns
Assembling contigs: 0%
Assembling contigs: 29.6%  ETA: 00:00:07
Assembling contigs: 39.8%  ETA: 00:03:33
Assembling contigs: 50%  ETA: 00:05:43
Assembling contigs: 57.5%  ETA: 00:11:18
Assembling contigs: 60.1%  ETA: 00:31:25
Assembling contigs: 62.9%  ETA: 00:25:45
Assembling contigs: 64.6%  ETA: 00:41:32
Assembling contigs: 66.3%  ETA: 00:41:28
Assembling contigs: 68.5%  ETA: 00:28:08
Assembling contigs: 69.9%  ETA: 00:42:22
Assembling contigs: 70.7%  ETA: 01:13:22
Assembling contigs: 70.8%  ETA: 10:41:35
Assembling contigs: 71.3%  ETA: 02:11:25
Assembling contigs: 71.4%  ETA: 06:11:12
Assembling contigs: 71.9%  ETA: 01:57:02
Assembling contigs: 72.3%  ETA: 02:22:38
Assembling contigs: 72.7%  ETA: 02:13:12
Assembling contigs: 74.2%  ETA: 00:35:10

Since 19 hours now.

I'm using the version below of mixcr to be able to use the command 10x-sc-xcr-vdj-gemx-v3 that match the 10x chemistry of my data.

MiXCR v4.7.0-345-develop (built Fri Apr 03 23:02:51 CEST 2026; rev=a707c7751b; branch=develop; host=runnervm727z3)
RepSeq.IO v2.5.0-26-master (rev=ec31c06fb1)
MiLib v3.5.0-20-master (rev=5c9a487780)
Built-in V/D/J/C library: repseqio.v6.3

Exact MiXCR commands

(pasted above)

MiXCR report files

I don't have a report for assembleContigs because it didn't complete yet. Do you need anothe report?

Thanks a lot in advance for your help!

[mizraelson]

Hi, this is most likely a memory issue. Is it possible to give MiXCR more memory? -Xmx200g?

[ericavalentini]

Yes, it worked. Thanks a lot!