Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/6007d1d5f89ef2aecf745e63181d61/truth_variants.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/607f16440c89581e40dbc10bad76fb/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1b409da7bf08ca9d1e19dad1032730/test_variants.tsv
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed
Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/tso500/pepe_blacklist_sorted_hg38.bed
Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/tso500/TruSight_Oncology_500_Manifest_hg38.st.mrg.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/607f16440c89581e40dbc10bad76fb/.command.run
==> STAGING COMPLETE (10 inputs)
mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-olids71_ 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.
Loading test variants...
89372 test variants loaded
Loading truth variants...
35619 truth variants loaded
3959 PASS truth variants total
2862 PASS truth variants in PON (excluded)
0 PASS truth variants in POT (excluded)
0 PASS truth variants in blacklist (excluded)
138 truth variants after filtering (PASS, not in_pon, not in_pot, not in_blacklist, is_exome, in_truth_panel)
60967 test variants in PON (excluded)
285 test variants in POT (excluded)
37 test variants after region filter (PASS, not in_pon, not in_pot, not in_blacklist, is_exome, in_truth_panel)
Building test variant lookups from extracted test table...
3 samples indexed, 89372 total variants
Performing bi-directional germline reclassification...
Input: 31 somatic, 107 germline candidates
Rule 2 (somatic→germline): 5 removed
somatic_to_germline: 5
Rule 1 (germline→somatic): 10 rescued
36 truth variants remaining after reclassification
Truth expanded from 36 to 36 rows (for 3 specimens with test data)
Classification summary (3 samples):
SNV TP: 30
SNV FN: 4
SNV FP: 7
INDEL TP: 0
INDEL FN: 1
INDEL FP: 0
Protein-level matching: 0 FN/FP pairs reclassified as TP (0 exact, 0 frameshift-within-2aa)
FN status breakdown (6 total):
called_hard_filtered: 4 (66.7%)
: 2 (33.3%)
Classification after protein matching (3 samples):
SNV boosted: TP=30 FP=7 FN=3 Sens=0.9091 PPV=0.8108
SNV nonboosted: TP=0 FP=0 FN=1 Sens=0.0000 PPV=0.0000
INDEL boosted: TP=0 FP=0 FN=1 Sens=0.0000 PPV=0.0000
INDEL nonboosted: TP=0 FP=0 FN=0 Sens=0.0000 PPV=0.0000
Wrote germline_reclassified.tsv
Wrote germline_rescued_to_somatic.tsv
Computing region sizes for specificity...
Boosted ROI: 1,251,199 bp
Nonboosted ROI: 32,944 bp
[E::idx_find_and_load] Could not retrieve index file for 'pon_tnseq_42_curated_v4.vcf.gz'
[E::idx_find_and_load] Could not retrieve index file for 'pon_tnseq_42_curated_v4.vcf.gz'
PON sites in boosted: 4,632
PON sites in nonboosted: 217
[E::idx_find_and_load] Could not retrieve index file for 'aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz'
[E::idx_find_and_load] Could not retrieve index file for 'aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz'
POT sites in boosted: 3
POT sites in nonboosted: 0
Wrote variant_filter_waterfall.tsv
source stage snvs indels total
truth total_loaded 28599 6952 35551
truth removed_not_pass 24899 6761 31660
truth removed_in_pon 2720 96 2816
truth removed_in_pot 0 0 0
truth removed_in_blacklist 0 0 0
truth removed_not_exome 851 87 938
truth removed_not_in_truth_panel 0 0 0
truth entering_comparison 129 8 137
test total_loaded 61791 27581 89372
test removed_not_pass 59478 27527 87005
test removed_in_pon 1 0 1
test removed_in_pot 0 0 0
test removed_in_blacklist 1 0 1
test removed_not_exome 1200 36 1236
test removed_not_in_truth_panel 1074 18 1092
test entering_comparison 37 0 37
Wrote aggregated_metrics.csv
Saved comparison/vaf_bin_sensitivity_ppv.png
=== SNV Sensitivity -- boosted ===
0-2.5%: 0.0000 [0.0000, 0.7935] (n=1, tp=0)
2.5-5%: 0.0000 [0.0000, 0.6576] (n=2, tp=0)
5-7.5%: 1.0000 [0.5101, 1.0000] (n=4, tp=4)
7.5-10%: 1.0000 [0.2065, 1.0000] (n=1, tp=1)
10-15%: N/A (n=0)
15-25%: 1.0000 [0.5101, 1.0000] (n=4, tp=4)
25-50%: 1.0000 [0.7412, 1.0000] (n=11, tp=11)
50-100%: 1.0000 [0.7225, 1.0000] (n=10, tp=10)
=== SNV PPV -- boosted ===
0-2.5%: 0.0000 [0.0000, 0.3903] (n=6, tp=0)
2.5-5%: 0.0000 [0.0000, 0.7935] (n=1, tp=0)
5-7.5%: 1.0000 [0.4385, 1.0000] (n=3, tp=3)
7.5-10%: 1.0000 [0.3424, 1.0000] (n=2, tp=2)
10-15%: N/A (n=0)
15-25%: 1.0000 [0.4385, 1.0000] (n=3, tp=3)
25-50%: 1.0000 [0.7719, 1.0000] (n=13, tp=13)
50-100%: 1.0000 [0.7009, 1.0000] (n=9, tp=9)
=== SNV Sensitivity -- nonboosted ===
0-2.5%: 0.0000 [0.0000, 0.7935] (n=1, tp=0)
2.5-5%: N/A (n=0)
5-7.5%: N/A (n=0)
7.5-10%: N/A (n=0)
10-15%: N/A (n=0)
15-25%: N/A (n=0)
25-50%: N/A (n=0)
50-100%: N/A (n=0)
=== SNV PPV -- nonboosted ===
0-2.5%: N/A (n=0)
2.5-5%: N/A (n=0)
5-7.5%: N/A (n=0)
7.5-10%: N/A (n=0)
10-15%: N/A (n=0)
15-25%: N/A (n=0)
25-50%: N/A (n=0)
50-100%: N/A (n=0)
=== INDEL Sensitivity -- boosted ===
0-2.5%: 0.0000 [0.0000, 0.7935] (n=1, tp=0)
2.5-5%: N/A (n=0)
5-7.5%: N/A (n=0)
7.5-10%: N/A (n=0)
10-15%: N/A (n=0)
15-25%: N/A (n=0)
25-50%: N/A (n=0)
50-100%: N/A (n=0)
=== INDEL PPV -- boosted ===
0-2.5%: N/A (n=0)
2.5-5%: N/A (n=0)
5-7.5%: N/A (n=0)
7.5-10%: N/A (n=0)
10-15%: N/A (n=0)
15-25%: N/A (n=0)
25-50%: N/A (n=0)
50-100%: N/A (n=0)
=== INDEL Sensitivity -- nonboosted ===
0-2.5%: N/A (n=0)
2.5-5%: N/A (n=0)
5-7.5%: N/A (n=0)
7.5-10%: N/A (n=0)
10-15%: N/A (n=0)
15-25%: N/A (n=0)
25-50%: N/A (n=0)
50-100%: N/A (n=0)
=== INDEL PPV -- nonboosted ===
0-2.5%: N/A (n=0)
2.5-5%: N/A (n=0)
5-7.5%: N/A (n=0)
7.5-10%: N/A (n=0)
10-15%: N/A (n=0)
15-25%: N/A (n=0)
25-50%: N/A (n=0)
50-100%: N/A (n=0)
Wrote filter_summary.json
mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-s8edj46y 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.