[root@DC3-21-007 ~]# cellranger testrun --id=test_install_check --localcores=1 --localmem=1 


Martian Runtime - v4.0.12 

2024-10-10 01:00:26 [runtime] Reattaching in local mode. 

Serving UI at http://DC3-21-007:46403?auth=LVlPSXQpkh1PyU2nMsGXmzpSlvhIfl7dkpXRnkIPlHE 

 
2024-10-10 01:00:26 [runtime] (reset-partial)   ID.test_install_check.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT.fork0.chnk0 

2024-10-10 01:00:26 [runtime] (reset-partial)   ID.test_install_check.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT_LOCAL.fork0.chnk0 

2024-10-10 01:00:26 [runtime] Found orphaned local stage: ID.test_install_check.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT_LOCAL 

2024-10-10 01:00:26 [runtime] Found orphaned local stage: ID.test_install_check.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT 

 
[error] Pipestance failed. Error log at: 

test_install_check/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL/fork0/chnk0-ua73906b6aa/_errors 

 
Log message: 

Traceback (most recent call last): 

  File "/root/cellranger-8.0.1/external/martian/adapters/python/martian_shell.py", line 454, in __init__ 

    self._module = __import__(os.path.basename(stagecode_path)) 

  File "/root/cellranger-8.0.1/mro/rna/stages/common/cellranger_preflight/__init__.py", line 8, in <module> 

    import cellranger.preflight as cr_preflight 

  File "/root/cellranger-8.0.1/lib/python/cellranger/preflight.py", line 17, in <module> 

    import cellranger.rna.feature_ref as rna_feature_ref 

  File "/root/cellranger-8.0.1/lib/python/cellranger/rna/feature_ref.py", line 24, in <module> 

    from cellranger.feature_ref import ( 

  File "/root/cellranger-8.0.1/lib/python/cellranger/feature_ref.py", line 21, in <module> 

    from cellranger.feature.antigen.specificity import MHC_ALLELE, TARGETING_ANTIGEN 

  File "/root/cellranger-8.0.1/lib/python/cellranger/feature/antigen/specificity.py", line 16, in <module> 

    from scipy.stats import beta 

  File "/root/cellranger-8.0.1/external/anaconda/lib/python3.10/site-packages/scipy/stats/__init__.py", line 485, in <module> 

    from ._stats_py import * 

  File "/root/cellranger-8.0.1/external/anaconda/lib/python3.10/site-packages/scipy/stats/_stats_py.py", line 46, in <module> 

    from . import distributions 

  File "/root/cellranger-8.0.1/external/anaconda/lib/python3.10/site-packages/scipy/stats/distributions.py", line 10, in <module> 

    from . import _continuous_distns 

  File "/root/cellranger-8.0.1/external/anaconda/lib/python3.10/site-packages/scipy/stats/_continuous_distns.py", line 32, in <module> 

    import scipy.stats._boost as _boost 

  File "/root/cellranger-8.0.1/external/anaconda/lib/python3.10/site-packages/scipy/stats/_boost/__init__.py", line 1, in <module> 

    from scipy.stats._boost.beta_ufunc import ( 

SystemError: initialization of beta_ufunc raised unreported exception 

 
Waiting 6 seconds for UI to do final refresh. 

Pipestance failed. Use --noexit option to keep UI running after failure. 



2024-10-10 01:00:34 Shutting down. 

Saving pipestance info to "test_install_check/test_install_check.mri.tgz" 

For assistance, upload this file to 10x Genomics by running: 

 
cellranger upload <your_email> "test_install_check/test_install_check.mri.tgz"