File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/976a02fcd19e2293af083061850f48/.command.log
Size
2.4 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT (rna_s1221_S42)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/766ed0fa6ab7fc7804b3325c3e380b/rna_s1221_S42.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/976a02fcd19e2293af083061850f48/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/9be1f123b0608b1c13f91ed1e17d4a/rna_s1221_S42.arriba.fusions.filtered_pass_only.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/hgnc/hgnc_complete_set.txt
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/hgnc/HGNC-DB-timestamp.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/174ceeb5cff166500f41a53b602b64/rna_s1221_S42_fusionreport_index.html
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/174ceeb5cff166500f41a53b602b64/rna_s1221_S42.fusions.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/976a02fcd19e2293af083061850f48/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/a69066590adf34c0c25efc87b4bc22/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
==> STAGING COMPLETE (9 inputs)

Traceback (most recent call last):
  File "/tmp/nxf.RXWZCX7QDK/nextflow-bin/vcf_collect.py", line 7, in <module>
    import pandas as pd
  File "/usr/local/lib/python3.11/site-packages/pandas/__init__.py", line 22, in <module>
    from pandas.compat import is_numpy_dev as _is_numpy_dev  # pyright: ignore # noqa:F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/pandas/compat/__init__.py", line 18, in <module>
    from pandas.compat.numpy import (
  File "/usr/local/lib/python3.11/site-packages/pandas/compat/numpy/__init__.py", line 4, in <module>
    from pandas.util.version import Version
  File "/usr/local/lib/python3.11/site-packages/pandas/util/__init__.py", line 2, in <module>
    from pandas.util._decorators import (  # noqa:F401
  File "/usr/local/lib/python3.11/site-packages/pandas/util/_decorators.py", line 14, in <module>
    from pandas._libs.properties import cache_readonly
  File "/usr/local/lib/python3.11/site-packages/pandas/_libs/__init__.py", line 13, in <module>
    from pandas._libs.interval import Interval
  File "pandas/_libs/interval.pyx", line 1, in init pandas._libs.interval
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject