mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-n3ywe2vv 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 truth variants...
343 truth variants loaded
Loading test variants...
375 test variants loaded
Reclassifying germline variants...
het range: [0.4, 0.6], hom >= 0.9
Truth germline: 0
Test germline: 0
343 truth variants entering comparison
375 test variants entering comparison
Truth expanded to 343 rows for 3 specimens with test data
MNVs recovered via component SNVs: 0
Building VCF lookups from 3 files...
[E::idx_find_and_load] Could not retrieve index file for 'test_vcf_dir/1029_HN2-T1-TDNA-1_A23L5NJLT4_1_vs_1029_HN2-N1-BDNA-1_235YY7LT3_1.norm.vcf.gz'
1029_HN2-T1-TDNA-1_A23L5NJLT4_1_vs_1029_HN2-N1-BDNA-1_235YY7LT3_1: 55188 variants indexed
[E::idx_find_and_load] Could not retrieve index file for 'test_vcf_dir/1241_J22-T1-TDNA-1_A23NN2MLT4_1_vs_1241_J22-N1-BDNA-1_A23TY32LT4_1.norm.vcf.gz'
1241_J22-T1-TDNA-1_A23NN2MLT4_1_vs_1241_J22-N1-BDNA-1_A23TY32LT4_1: 28831 variants indexed
[E::idx_find_and_load] Could not retrieve index file for 'test_vcf_dir/869_B0C-T1-TDNA-1_A23FG3YLT4_1_vs_869_B0C-N1-BDNA-1_A23FG3YLT4_1.norm.vcf.gz'
869_B0C-T1-TDNA-1_A23FG3YLT4_1_vs_869_B0C-N1-BDNA-1_A23FG3YLT4_1: 44641 variants indexed
Classifying variants...
Classification summary (3 samples):
SNV TP: 262
SNV FN: 16
SNV FP: 53
INDEL TP: 54
INDEL FN: 11
INDEL FP: 6
SNV boosted: TP=206 FP=41 FN=7 Sens=0.9671 PPV=0.8340
SNV nonboosted: TP=56 FP=12 FN=9 Sens=0.8615 PPV=0.8235
INDEL boosted: TP=35 FP=4 FN=11 Sens=0.7609 PPV=0.8974
INDEL nonboosted: TP=19 FP=2 FN=0 Sens=1.0000 PPV=0.9048
FN reason breakdown (27 total):
filtered: 17 (63.0%)
not_called: 10 (37.0%)
Wrote variant_classification.tsv
Computing region sizes for specificity...
Boosted ROI: 1,251,200 bp
Nonboosted ROI: 402,392 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'
[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'
PON in boosted: 4,632
PON in nonboosted: 6,927
POT in boosted: 3
POT in nonboosted: 1
Wrote variant_filter_waterfall.tsv
source stage snvs indels mnvs total
truth loaded 278 65 0 343
truth removed_germline_reclassified 0 0 0 0
truth entering_comparison 278 65 0 343
test loaded 315 60 0 375
test removed_germline_reclassified 0 0 0 0
test entering_comparison 315 60 0 375
Wrote aggregated_metrics.csv
Saved comparison/vaf_bin_sensitivity_ppv.png
=== SNV Sensitivity -- boosted ===
0-5%: 0.9348 [0.8250, 0.9776] (n=46, tp=43)
5-10%: 0.9894 [0.9422, 0.9981] (n=94, tp=93)
10-20%: 0.9706 [0.8990, 0.9919] (n=68, tp=66)
20-50%: 1.0000 [0.5101, 1.0000] (n=4, tp=4)
>50%: 0.0000 [0.0000, 0.7935] (n=1, tp=0)
=== SNV PPV -- boosted ===
0-5%: 0.6349 [0.5115, 0.7428] (n=63, tp=40)
5-10%: 0.9244 [0.8625, 0.9597] (n=119, tp=110)
10-20%: 0.8966 [0.7921, 0.9517] (n=58, tp=52)
20-50%: 0.6667 [0.3000, 0.9032] (n=6, tp=4)
>50%: 0.0000 [0.0000, 0.7935] (n=1, tp=0)
=== SNV Sensitivity -- nonboosted ===
0-5%: 0.7000 [0.3968, 0.8922] (n=10, tp=7)
5-10%: 0.8889 [0.7469, 0.9559] (n=36, tp=32)
10-20%: 0.8947 [0.6861, 0.9706] (n=19, tp=17)
20-50%: N/A (n=0)
>50%: N/A (n=0)
=== SNV PPV -- nonboosted ===
0-5%: 0.3889 [0.2031, 0.6138] (n=18, tp=7)
5-10%: 0.9706 [0.8508, 0.9948] (n=34, tp=33)
10-20%: 1.0000 [0.8064, 1.0000] (n=16, tp=16)
20-50%: N/A (n=0)
>50%: N/A (n=0)
=== INDEL Sensitivity -- boosted ===
0-5%: 0.2000 [0.0362, 0.6245] (n=5, tp=1)
5-10%: 0.7407 [0.5532, 0.8683] (n=27, tp=20)
10-20%: 1.0000 [0.7575, 1.0000] (n=12, tp=12)
20-50%: 1.0000 [0.3424, 1.0000] (n=2, tp=2)
>50%: N/A (n=0)
=== INDEL PPV -- boosted ===
0-5%: 1.0000 [0.2065, 1.0000] (n=1, tp=1)
5-10%: 0.9130 [0.7320, 0.9758] (n=23, tp=21)
10-20%: 0.8462 [0.5777, 0.9567] (n=13, tp=11)
20-50%: 1.0000 [0.3424, 1.0000] (n=2, tp=2)
>50%: N/A (n=0)
=== INDEL Sensitivity -- nonboosted ===
0-5%: N/A (n=0)
5-10%: 1.0000 [0.6457, 1.0000] (n=7, tp=7)
10-20%: 1.0000 [0.7412, 1.0000] (n=11, tp=11)
20-50%: 1.0000 [0.2065, 1.0000] (n=1, tp=1)
>50%: N/A (n=0)
=== INDEL PPV -- nonboosted ===
0-5%: 1.0000 [0.2065, 1.0000] (n=1, tp=1)
5-10%: 0.8571 [0.4869, 0.9743] (n=7, tp=6)
10-20%: 0.9167 [0.6461, 0.9851] (n=12, tp=11)
20-50%: 1.0000 [0.2065, 1.0000] (n=1, tp=1)
>50%: N/A (n=0)
mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-e29p56d7 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.