.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT (custom_Sig_18_tumor_normal)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/9ba574c664b055eff4682e2fd15740/.command.log
Size: 1.3 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT (custom_Sig_18_tumor_normal)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/9ba574c664b055eff4682e2fd15740/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/dddea1b767e10496f387cf9f25520d/Sig_18_tissue.recalibrated.somatic.call.cns
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/9ba574c664b055eff4682e2fd15740/.command.run
==> STAGING COMPLETE (3 inputs)

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1a88wpd2 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 Sig_18_tissue.recalibrated.somatic.call as male
Wrote custom_Sig_18_tumor_normal.cnvcall.vcf
Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gjais8ol 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