Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/701ce861cfc5a1e0e1759eb332e7f9/HCC1395_tumor.recalibrated.cns
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/701ce861cfc5a1e0e1759eb332e7f9/HCC1395_tumor.recalibrated.cnr
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/3ab5a7a32117c9dbc74856e5b5423f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/3ab5a7a32117c9dbc74856e5b5423f/.command.run
==> STAGING COMPLETE (4 inputs)

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rfhen3r1 because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Fontconfig error: No writable cache directories
No chrX found in sample; is the input truncated?
Treating sample HCC1395_tumor.recalibrated as male
No chrX found in sample; is the input truncated?
No chrX found in sample; is the input truncated?
No chrX found in sample; is the input truncated?
Found 0 gene-level gains and losses
Wrote HCC1395_tumor.recalibrated.genemetrics.tsv
Matplotlib created a temporary config/cache directory at /tmp/matplotlib-jaubzd19 because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Fontconfig error: No writable cache directories