File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/9ef20cd03cd6bb9f16525ed2e17902/.command.err
Size
2.0 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:GERMLINE_CNV (germline_control_2)
Attempt

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mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-ngni5mva because there was an issue with the default path (/.config/matplotlib); 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.
2026-06-06 04:55:37,254 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading input file: NA12878_c_0002_gDNA_0002_B23KGCJLT4_1_probe_sample.parquet
2026-06-06 04:55:37,340 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading reference genome FASTA file: Homo_sapiens_assembly38.fasta
2026-06-06 04:55:47,576 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Filtered out 18367 probes with mask flags (mask_probes_low, mask_probes_blacklist)
2026-06-06 04:55:47,576 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Failed probes (mask_probes_low or mask_probe_model_failed): 16147
2026-06-06 04:55:47,576 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Remaining probes: 444627
2026-06-06 04:55:47,581 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Single sample — skipping batch FC statistics
2026-06-06 04:55:47,586 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processing 1 samples with 1 threads
2026-06-06 04:56:03,963 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processed NA12878_c_0002_gDNA_0002_B23KGCJLT4_1: 152 deletions, 97 duplications
2026-06-06 04:56:03,964 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - 
Processing complete!
2026-06-06 04:56:03,964 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total samples successfully processed: 1
2026-06-06 04:56:03,964 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of samples failed QC: 0
2026-06-06 04:56:03,964 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of probes failed QC: 16147
2026-06-06 04:56:03,964 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total deletions: 152
2026-06-06 04:56:03,964 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total duplications: 97