Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/bd739054ad9fe0a5795042d2575e1d/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/bd739054ad9fe0a5795042d2575e1d/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
Matplotlib created a temporary cache directory at /var/tmp/matplotlib-7frxdo0i 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
CNVkit 0.9.10
Detected file format: bed
Splitting large targets
Wrote ./xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.target.bed with 2478 regions
Wrote ./xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.antitarget.bed with 501 regions
Building a copy number reference from normal samples...
Processing reads in Sig_18_Blood.recalibrated.bam
Processing reads in Sig_18_Blood.recalibrated.bam
Time: 1.548 seconds (306685 reads/sec, 324 bins/sec)
Summary: #bins=501, #reads=474698, mean=947.5020, min=0.0, max=99651.66804979253
Percent reads in regions: 19.131 (of 2481264 mapped)
Wrote ./Sig_18_Blood.recalibrated.antitargetcoverage.cnn with 501 regions
Time: 10.113 seconds (130419 reads/sec, 245 bins/sec)
Summary: #bins=2478, #reads=1318978, mean=532.2754, min=0.7219917012448133, max=5158.116182572614
Percent reads in regions: 53.158 (of 2481264 mapped)
Wrote ./Sig_18_Blood.recalibrated.targetcoverage.cnn with 2478 regions
No chrX found in sample; is the input truncated?
No chrX found in sample; is the input truncated?
Loading ./Sig_18_Blood.recalibrated.targetcoverage.cnn
Calculating GC and RepeatMasker content in Homo_sapiens_assembly38.fasta ...
Extracting sequences from chromosome chr21
Correcting for GC bias...
Correcting for density bias...
Loading ./Sig_18_Blood.recalibrated.antitargetcoverage.cnn
Calculating GC and RepeatMasker content in Homo_sapiens_assembly38.fasta ...
Extracting sequences from chromosome chr21
Correcting for GC bias...
Correcting for RepeatMasker bias...
Calculating average bin coverages
Calculating bin spreads
Targets: 349 (14.08%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)
- chr21:5128214-5128354 log2=0.368 spread=0.546 rmask=nan
" chr21:5590019-5590218 log2=0.710 spread=1.053 rmask=nan
" chr21:6119024-6119240 log2=0.125 spread=0.185 rmask=nan
" chr21:6121144-6121519 log2=0.015 spread=0.023 rmask=nan
" chr21:6447736-6447777 log2=-0.364 spread=0.540 rmask=nan
" chr21:6484769-6484916 log2=0.936 spread=1.387 rmask=nan
" chr21:6487107-6487205 log2=-0.828 spread=1.228 rmask=nan
" chr21:6495993-6496080 log2=0.954 spread=1.414 rmask=nan
" chr21:10413740-10413754 log2=0.867 spread=1.286 rmask=nan
" chr21:10454134-10454296 log2=0.890 spread=1.319 rmask=nan
" chr21:10462836-10462886 log2=1.082 spread=1.604 rmask=nan
" chr21:10538724-10538734 log2=0.739 spread=1.096 rmask=nan
" chr21:10552657-10552716 log2=0.982 spread=1.456 rmask=nan
" chr21:10559494-10559544 log2=0.780 spread=1.156 rmask=nan
" chr21:10567670-10567789 log2=0.922 spread=1.368 rmask=nan
" chr21:10569437-10569536 log2=0.828 spread=1.227 rmask=nan
" chr21:10570485-10570549 log2=0.780 spread=1.156 rmask=nan
" chr21:10590462-10590523 log2=0.844 spread=1.251 rmask=nan
" chr21:10592293-10592373 log2=1.015 spread=1.506 rmask=nan
" chr21:10595982-10596087 log2=0.899 spread=1.333 rmask=nan
" chr21:10598015-10598094 log2=1.039 spread=1.540 rmask=nan
" chr21:10602058-10602150 log2=0.910 spread=1.350 rmask=nan
" chr21:10603562-10603632 log2=0.892 spread=1.322 rmask=nan
" chr21:10605417-10605552 log2=0.725 spread=1.075 rmask=nan
" chr21:13610229-13610488 log2=-1.661 spread=2.463 rmask=nan
" chr21:13610489-13610749 log2=-3.290 spread=4.878 rmask=nan
" chr21:13615123-13615237 log2=-0.831 spread=1.233 rmask=nan
" chr21:13615397-13615570 log2=-1.030 spread=1.527 rmask=nan
" chr21:13620158-13620295 log2=-0.924 spread=1.369 rmask=nan
" chr21:13622805-13622875 log2=-0.473 spread=0.702 rmask=nan
" chr21:13639515-13639638 log2=-1.524 spread=2.260 rmask=nan
" chr21:13641345-13641566 log2=-1.919 spread=2.845 rmask=nan
" chr21:14592622-14592639 log2=-0.016 spread=0.024 rmask=nan
" chr21:14612876-14612913 log2=0.383 spread=0.568 rmask=nan
" chr21:14615976-14616016 log2=0.299 spread=0.443 rmask=nan
" chr21:18245224-18245302 log2=0.008 spread=0.012 rmask=nan
" chr21:18359757-18359863 log2=0.155 spread=0.230 rmask=nan
" chr21:18397879-18397946 log2=0.437 spread=0.648 rmask=nan
" chr21:21385604-21385608 log2=0.493 spread=0.731 rmask=nan
" chr21:25639822-25639888 log2=-0.208 spread=0.309 rmask=nan
" chr21:25714640-25714672 log2=0.023 spread=0.034 rmask=nan
" chr21:26170564-26170620 log2=-0.217 spread=0.322 rmask=nan
" chr21:26844225-26844467 log2=-0.300 spread=0.445 rmask=nan
" chr21:26844711-26844954 log2=-0.080 spread=0.118 rmask=nan
" chr21:26965564-26965839 log2=-0.307 spread=0.455 rmask=nan
" chr21:26966116-26966391 log2=-0.023 spread=0.034 rmask=nan
" chr21:29040609-29040687 log2=0.084 spread=0.125 rmask=nan
" chr21:29091501-29091576 log2=-1.910 spread=2.832 rmask=nan
" chr21:31559261-31559595 log2=-0.366 spread=0.543 rmask=nan
" chr21:31705423-31705467 log2=0.192 spread=0.285 rmask=nan
" chr21:31873675-31873935 log2=-0.071 spread=0.105 rmask=nan
" chr21:32392769-32392910 log2=-0.018 spread=0.027 rmask=nan
" chr21:32645646-32645789 log2=0.252 spread=0.374 rmask=nan
" chr21:32769814-32769942 log2=0.054 spread=0.079 rmask=nan
" chr21:32771326-32771668 log2=-0.209 spread=0.309 rmask=nan
" chr21:33027349-33027591 log2=-0.399 spread=0.591 rmask=nan
" chr21:33027592-33027834 log2=-0.375 spread=0.556 rmask=nan
" chr21:33070247-33070518 log2=-0.140 spread=0.208 rmask=nan
" chr21:33070519-33070790 log2=-0.765 spread=1.135 rmask=nan
" chr21:33070791-33071062 log2=-0.600 spread=0.889 rmask=nan
" chr21:33403544-33403616 log2=-0.013 spread=0.020 rmask=nan
" chr21:33557546-33557551 log2=0.214 spread=0.317 rmask=nan
" chr21:33588321-33588641 log2=0.046 spread=0.068 rmask=nan
" chr21:33915728-33915763 log2=-0.024 spread=0.035 rmask=nan
" chr21:34614760-34615011 log2=-0.015 spread=0.023 rmask=nan
" chr21:34669389-34669662 log2=-0.434 spread=0.643 rmask=nan
" chr21:34669663-34669937 log2=-0.299 spread=0.443 rmask=nan
" chr21:34669938-34670212 log2=-0.072 spread=0.106 rmask=nan
" chr21:34670213-34670487 log2=-0.334 spread=0.495 rmask=nan
" chr21:34670488-34670762 log2=-0.399 spread=0.592 rmask=nan
" chr21:34787802-34788068 log2=1.076 spread=1.595 rmask=nan
" chr21:34788069-34788336 log2=1.112 spread=1.649 rmask=nan
" chr21:34788337-34788604 log2=1.078 spread=1.599 rmask=nan
" chr21:34788605-34788872 log2=1.079 spread=1.600 rmask=nan
" chr21:34788873-34789139 log2=1.134 spread=1.681 rmask=nan
" chr21:34789140-34789407 log2=1.122 spread=1.664 rmask=nan
" chr21:34789408-34789675 log2=1.186 spread=1.758 rmask=nan
" chr21:34789676-34789943 log2=1.117 spread=1.656 rmask=nan
" chr21:34789944-34790211 log2=1.033 spread=1.531 rmask=nan
" chr21:34790212-34790478 log2=1.040 spread=1.541 rmask=nan
" chr21:34790479-34790746 log2=0.870 spread=1.290 rmask=nan
" chr21:34790747-34791014 log2=0.811 spread=1.203 rmask=nan
" chr21:34791015-34791282 log2=0.986 spread=1.462 rmask=nan
" chr21:34791283-34791549 log2=0.864 spread=1.281 rmask=nan
" chr21:34791550-34791817 log2=1.056 spread=1.565 rmask=nan
" chr21:34791818-34792085 log2=0.638 spread=0.947 rmask=nan
" chr21:34792086-34792353 log2=0.434 spread=0.644 rmask=nan
" chr21:34792354-34792621 log2=0.869 spread=1.288 rmask=nan
" chr21:34821280-34821487 log2=1.301 spread=1.928 rmask=nan
" chr21:34821488-34821696 log2=0.948 spread=1.406 rmask=nan
" chr21:34834409-34834601 log2=0.998 spread=1.479 rmask=nan
" chr21:34859439-34859439 log2=1.117 spread=1.656 rmask=nan
" chr21:34859473-34859578 log2=0.787 spread=1.167 rmask=nan
" chr21:34880546-34880715 log2=0.709 spread=1.051 rmask=nan
" chr21:34886841-34887104 log2=0.985 spread=1.461 rmask=nan
" chr21:34887369-34887632 log2=1.028 spread=1.524 rmask=nan
" chr21:34887633-34887897 log2=1.090 spread=1.616 rmask=nan
" chr21:34887898-34888161 log2=1.000 spread=1.483 rmask=nan
" chr21:34888162-34888425 log2=1.004 spread=1.489 rmask=nan
" chr21:34888426-34888690 log2=1.019 spread=1.511 rmask=nan
" chr21:35048842-35049092 log2=1.145 spread=1.698 rmask=nan
" chr21:35049093-35049344 log2=1.318 spread=1.953 rmask=nan
" chr21:35220968-35221087 log2=0.675 spread=1.001 rmask=nan
" chr21:36041807-36041888 log2=0.232 spread=0.343 rmask=nan
" chr21:36320265-36320303 log2=0.046 spread=0.068 rmask=nan
" chr21:36461216-36461455 log2=-0.710 spread=1.052 rmask=nan
" chr21:36709168-36709250 log2=0.009 spread=0.014 rmask=nan
" chr21:36747665-36747878 log2=-0.598 spread=0.887 rmask=nan
" chr21:36747879-36748092 log2=-0.651 spread=0.965 rmask=nan
" chr21:36966444-36966638 log2=-0.109 spread=0.161 rmask=nan
" chr21:37006773-37006876 log2=-0.016 spread=0.024 rmask=nan
" chr21:37073429-37073483 log2=-0.268 spread=0.397 rmask=nan
" chr21:37090233-37090286 log2=-0.075 spread=0.110 rmask=nan
" chr21:38121128-38121255 log2=-0.733 spread=1.087 rmask=nan
" chr21:38299826-38300107 log2=-0.739 spread=1.096 rmask=nan
" chr21:38380028-38380286 log2=1.230 spread=1.823 rmask=nan
" chr21:38380287-38380546 log2=0.873 spread=1.295 rmask=nan
" chr21:38380547-38380806 log2=1.169 spread=1.734 rmask=nan
" chr21:38380807-38381065 log2=0.973 spread=1.442 rmask=nan
" chr21:38381066-38381325 log2=0.918 spread=1.361 rmask=nan
" chr21:38381326-38381585 log2=0.909 spread=1.348 rmask=nan
" chr21:38381586-38381845 log2=0.981 spread=1.455 rmask=nan
" chr21:38381846-38382104 log2=1.025 spread=1.520 rmask=nan
" chr21:38382105-38382364 log2=1.023 spread=1.517 rmask=nan
" chr21:38382365-38382624 log2=1.223 spread=1.814 rmask=nan
" chr21:38382885-38383143 log2=1.012 spread=1.500 rmask=nan
" chr21:38383144-38383403 log2=0.968 spread=1.435 rmask=nan
" chr21:38383404-38383663 log2=0.925 spread=1.372 rmask=nan
" chr21:38383664-38383923 log2=0.881 spread=1.306 rmask=nan
" chr21:38390995-38391042 log2=0.694 spread=1.029 rmask=nan
" chr21:38423410-38423561 log2=0.769 spread=1.139 rmask=nan
" chr21:38584845-38584945 log2=0.781 spread=1.158 rmask=nan
" chr21:38660523-38660667 log2=0.878 spread=1.302 rmask=nan
" chr21:38661659-38661694 log2=0.734 spread=1.088 rmask=nan
" chr21:38805971-38806120 log2=0.175 spread=0.260 rmask=nan
" chr21:39313443-39313491 log2=-0.021 spread=0.031 rmask=nan
" chr21:39380523-39380552 log2=-0.040 spread=0.059 rmask=nan
" chr21:39788167-39788188 log2=0.258 spread=0.383 rmask=nan
" chr21:41168264-41168575 log2=0.044 spread=0.065 rmask=nan
" chr21:41464388-41464639 log2=1.057 spread=1.567 rmask=nan
" chr21:41464640-41464891 log2=1.144 spread=1.696 rmask=nan
" chr21:41464892-41465143 log2=1.119 spread=1.659 rmask=nan
" chr21:41465144-41465396 log2=0.950 spread=1.408 rmask=nan
" chr21:41465649-41465900 log2=1.086 spread=1.610 rmask=nan
" chr21:41465901-41466153 log2=1.088 spread=1.613 rmask=nan
" chr21:41471806-41471981 log2=0.828 spread=1.227 rmask=nan
" chr21:41473325-41473496 log2=0.699 spread=1.037 rmask=nan
" chr21:41476577-41476620 log2=0.713 spread=1.058 rmask=nan
" chr21:41480933-41481212 log2=1.084 spread=1.608 rmask=nan
" chr21:41481213-41481492 log2=0.980 spread=1.453 rmask=nan
" chr21:41481493-41481772 log2=1.123 spread=1.665 rmask=nan
" chr21:41482133-41482432 log2=1.076 spread=1.595 rmask=nan
" chr21:41482433-41482732 log2=1.177 spread=1.745 rmask=nan
" chr21:41482733-41483032 log2=0.947 spread=1.403 rmask=nan
" chr21:41483033-41483332 log2=1.059 spread=1.570 rmask=nan
" chr21:41483573-41483812 log2=1.101 spread=1.632 rmask=nan
" chr21:41484173-41484472 log2=1.191 spread=1.766 rmask=nan
" chr21:41484473-41484772 log2=1.241 spread=1.840 rmask=nan
" chr21:41484773-41485072 log2=0.957 spread=1.419 rmask=nan
" chr21:41485073-41485372 log2=1.090 spread=1.616 rmask=nan
" chr21:41485733-41486032 log2=0.918 spread=1.361 rmask=nan
" chr21:41486033-41486332 log2=1.137 spread=1.686 rmask=nan
" chr21:41486573-41486872 log2=0.988 spread=1.465 rmask=nan
" chr21:41486873-41487172 log2=1.071 spread=1.588 rmask=nan
" chr21:41487173-41487472 log2=1.009 spread=1.496 rmask=nan
" chr21:41487473-41487772 log2=1.064 spread=1.577 rmask=nan
" chr21:41488133-41488372 log2=1.025 spread=1.520 rmask=nan
" chr21:41488373-41488612 log2=0.938 spread=1.391 rmask=nan
" chr21:41488973-41489252 log2=0.985 spread=1.460 rmask=nan
" chr21:41489253-41489532 log2=0.810 spread=1.201 rmask=nan
" chr21:41489533-41489812 log2=0.941 spread=1.396 rmask=nan
" chr21:41490173-41490412 log2=1.280 spread=1.898 rmask=nan
" chr21:41490413-41490652 log2=1.102 spread=1.633 rmask=nan
" chr21:41490893-41491132 log2=1.113 spread=1.650 rmask=nan
" chr21:41491493-41491732 log2=1.167 spread=1.730 rmask=nan
" chr21:41491733-41491972 log2=1.064 spread=1.577 rmask=nan
" chr21:41492213-41492492 log2=1.142 spread=1.693 rmask=nan
" chr21:41492493-41492772 log2=0.951 spread=1.410 rmask=nan
" chr21:41492773-41493052 log2=1.024 spread=1.518 rmask=nan
" chr21:41493053-41493332 log2=0.839 spread=1.244 rmask=nan
" chr21:41493333-41493612 log2=0.682 spread=1.010 rmask=nan
" chr21:41493613-41493892 log2=1.062 spread=1.575 rmask=nan
" chr21:41493893-41494172 log2=1.016 spread=1.506 rmask=nan
" chr21:41494453-41494732 log2=0.929 spread=1.377 rmask=nan
" chr21:41495093-41495332 log2=0.843 spread=1.250 rmask=nan
" chr21:41495693-41495962 log2=0.977 spread=1.448 rmask=nan
" chr21:41495963-41496232 log2=1.023 spread=1.516 rmask=nan
" chr21:41496233-41496502 log2=0.934 spread=1.385 rmask=nan
" chr21:41496503-41496772 log2=1.046 spread=1.550 rmask=nan
" chr21:41497133-41497394 log2=1.034 spread=1.533 rmask=nan
" chr21:41497395-41497657 log2=1.020 spread=1.512 rmask=nan
" chr21:41497658-41497919 log2=0.922 spread=1.368 rmask=nan
" chr21:41497920-41498182 log2=0.932 spread=1.382 rmask=nan
" chr21:41498183-41498444 log2=1.183 spread=1.754 rmask=nan
" chr21:41498445-41498707 log2=1.013 spread=1.502 rmask=nan
" chr21:41498708-41498969 log2=0.872 spread=1.293 rmask=nan
" chr21:41498970-41499232 log2=0.853 spread=1.265 rmask=nan
" chr21:41499233-41499494 log2=1.103 spread=1.635 rmask=nan
" chr21:41499495-41499757 log2=1.029 spread=1.526 rmask=nan
" chr21:41499758-41500019 log2=0.955 spread=1.416 rmask=nan
" chr21:41500020-41500282 log2=0.953 spread=1.413 rmask=nan
" chr21:41500283-41500544 log2=1.104 spread=1.637 rmask=nan
" chr21:41500545-41500807 log2=1.189 spread=1.764 rmask=nan
" chr21:41500808-41501069 log2=1.118 spread=1.658 rmask=nan
" chr21:41501070-41501332 log2=1.156 spread=1.714 rmask=nan
" chr21:41501693-41501962 log2=1.084 spread=1.608 rmask=nan
" chr21:41501963-41502232 log2=0.938 spread=1.391 rmask=nan
" chr21:41502233-41502502 log2=1.065 spread=1.580 rmask=nan
" chr21:41502503-41502772 log2=1.109 spread=1.645 rmask=nan
" chr21:41502773-41503042 log2=1.258 spread=1.865 rmask=nan
" chr21:41503043-41503312 log2=1.097 spread=1.627 rmask=nan
" chr21:41503313-41503582 log2=1.030 spread=1.526 rmask=nan
" chr21:41503583-41503852 log2=1.150 spread=1.705 rmask=nan
" chr21:41503853-41504122 log2=0.993 spread=1.472 rmask=nan
" chr21:41504123-41504392 log2=1.063 spread=1.576 rmask=nan
" chr21:41504393-41504662 log2=1.173 spread=1.740 rmask=nan
" chr21:41504663-41504932 log2=0.998 spread=1.480 rmask=nan
" chr21:41504933-41505202 log2=1.120 spread=1.661 rmask=nan
" chr21:41505203-41505472 log2=1.286 spread=1.907 rmask=nan
" chr21:41505473-41505742 log2=1.008 spread=1.494 rmask=nan
" chr21:41505743-41506012 log2=0.998 spread=1.480 rmask=nan
" chr21:41506013-41506282 log2=1.030 spread=1.527 rmask=nan
" chr21:41506283-41506552 log2=0.754 spread=1.118 rmask=nan
" chr21:41506553-41506822 log2=1.013 spread=1.502 rmask=nan
" chr21:41506823-41507092 log2=0.852 spread=1.263 rmask=nan
" chr21:41507093-41507362 log2=0.925 spread=1.371 rmask=nan
" chr21:41507633-41507902 log2=0.942 spread=1.397 rmask=nan
" chr21:41507903-41508172 log2=0.925 spread=1.371 rmask=nan
" chr21:41508173-41508442 log2=0.890 spread=1.319 rmask=nan
" chr21:41508443-41508712 log2=0.869 spread=1.289 rmask=nan
" chr21:41508713-41508982 log2=0.857 spread=1.271 rmask=nan
" chr21:41508983-41509252 log2=1.089 spread=1.615 rmask=nan
" chr21:41509613-41509852 log2=1.191 spread=1.766 rmask=nan
" chr21:41509853-41510092 log2=0.901 spread=1.336 rmask=nan
" chr21:41510093-41510332 log2=0.949 spread=1.407 rmask=nan
" chr21:41510453-41510692 log2=0.732 spread=1.085 rmask=nan
" chr21:41510693-41510932 log2=1.034 spread=1.534 rmask=nan
" chr21:41511173-41511406 log2=1.113 spread=1.651 rmask=nan
" chr21:41511407-41511640 log2=0.907 spread=1.344 rmask=nan
" chr21:41511641-41511874 log2=0.832 spread=1.234 rmask=nan
" chr21:41511875-41512108 log2=1.217 spread=1.804 rmask=nan
" chr21:41529974-41530218 log2=1.272 spread=1.885 rmask=nan
" chr21:41530986-41531116 log2=1.359 spread=2.015 rmask=nan
" chr21:41741418-41741707 log2=-0.691 spread=1.024 rmask=nan
" chr21:41878695-41878860 log2=-0.413 spread=0.612 rmask=nan
" chr21:41878996-41879140 log2=-0.369 spread=0.548 rmask=nan
" chr21:41953370-41953648 log2=-0.106 spread=0.157 rmask=nan
" chr21:42111157-42111433 log2=-0.093 spread=0.138 rmask=nan
" chr21:42855682-42855780 log2=-0.274 spread=0.406 rmask=nan
" chr21:43065203-43065272 log2=-2.407 spread=3.568 rmask=nan
" chr21:43067778-43067778 log2=-0.110 spread=0.163 rmask=nan
" chr21:43092957-43093249 log2=0.746 spread=1.106 rmask=nan
" chr21:43094655-43094788 log2=0.751 spread=1.114 rmask=nan
" chr21:43104315-43104548 log2=0.941 spread=1.395 rmask=nan
" chr21:43104549-43104783 log2=0.863 spread=1.279 rmask=nan
" chr21:43104784-43105017 log2=0.811 spread=1.202 rmask=nan
" chr21:43105018-43105252 log2=1.207 spread=1.789 rmask=nan
" chr21:43416742-43417117 log2=0.018 spread=0.026 rmask=nan
" chr21:43419021-43419237 log2=0.115 spread=0.171 rmask=nan
" chr21:43658061-43658096 log2=0.184 spread=0.273 rmask=nan
" chr21:43776204-43776269 log2=0.096 spread=0.142 rmask=nan
" chr21:44133698-44133838 log2=0.332 spread=0.492 rmask=nan
" chr21:44215383-44215613 log2=0.678 spread=1.005 rmask=nan
" chr21:44218009-44218244 log2=0.745 spread=1.104 rmask=nan
" chr21:44223473-44223752 log2=0.678 spread=1.005 rmask=nan
" chr21:44226057-44226325 log2=0.781 spread=1.158 rmask=nan
" chr21:44226326-44226593 log2=0.778 spread=1.153 rmask=nan
" chr21:44227132-44227400 log2=0.779 spread=1.154 rmask=nan
" chr21:44228476-44228744 log2=0.752 spread=1.116 rmask=nan
" chr21:44229552-44229820 log2=0.636 spread=0.943 rmask=nan
" chr21:44229821-44230089 log2=0.813 spread=1.206 rmask=nan
" chr21:44233077-44233316 log2=0.691 spread=1.024 rmask=nan
" chr21:44233557-44233806 log2=0.766 spread=1.136 rmask=nan
" chr21:44235312-44235562 log2=0.733 spread=1.087 rmask=nan
" chr21:44240804-44241124 log2=0.206 spread=0.306 rmask=nan
" chr21:44241125-44241446 log2=0.325 spread=0.483 rmask=nan
" chr21:44289988-44290068 log2=-0.049 spread=0.073 rmask=nan
" chr21:44292302-44292401 log2=-0.244 spread=0.362 rmask=nan
" chr21:44293789-44293910 log2=-0.211 spread=0.313 rmask=nan
" chr21:44294401-44294503 log2=-0.312 spread=0.463 rmask=nan
" chr21:44300106-44300190 log2=-0.106 spread=0.158 rmask=nan
" chr21:44424852-44424939 log2=-0.239 spread=0.354 rmask=nan
" chr21:44550691-44550946 log2=-0.717 spread=1.063 rmask=nan
" chr21:44550947-44551202 log2=-0.758 spread=1.124 rmask=nan
" chr21:44573759-44573999 log2=0.704 spread=1.043 rmask=nan
" chr21:44574241-44574481 log2=-0.936 spread=1.388 rmask=nan
" chr21:44574482-44574722 log2=-1.379 spread=2.045 rmask=nan
" chr21:44580035-44580306 log2=-0.764 spread=1.133 rmask=nan
" chr21:44580307-44580578 log2=-0.359 spread=0.532 rmask=nan
" chr21:44591661-44591935 log2=-0.785 spread=1.163 rmask=nan
" chr21:44591936-44592209 log2=-0.707 spread=1.048 rmask=nan
" chr21:44600900-44601177 log2=-0.770 spread=1.142 rmask=nan
" chr21:44601178-44601455 log2=-0.814 spread=1.207 rmask=nan
" chr21:44612361-44612620 log2=-0.697 spread=1.034 rmask=nan
" chr21:44697694-44697939 log2=-0.251 spread=0.372 rmask=nan
" chr21:44855210-44855256 log2=0.676 spread=1.002 rmask=nan
" chr21:44873502-44873616 log2=0.053 spread=0.079 rmask=nan
" chr21:44910725-44910782 log2=-0.043 spread=0.064 rmask=nan
" chr21:44940058-44940186 log2=0.300 spread=0.444 rmask=nan
" chr21:45405231-45405241 log2=0.027 spread=0.040 rmask=nan
" chr21:45405379-45405473 log2=0.470 spread=0.697 rmask=nan
" chr21:45456611-45456881 log2=-0.185 spread=0.274 rmask=nan
" chr21:45475476-45475535 log2=-0.308 spread=0.456 rmask=nan
" chr21:45477750-45477965 log2=0.036 spread=0.054 rmask=nan
" chr21:45478327-45478353 log2=0.265 spread=0.392 rmask=nan
" chr21:45480700-45480858 log2=-0.004 spread=0.006 rmask=nan
" chr21:45481963-45482025 log2=-0.207 spread=0.307 rmask=nan
" chr21:45486861-45486992 log2=-0.305 spread=0.452 rmask=nan
" chr21:45488418-45488444 log2=0.034 spread=0.050 rmask=nan
" chr21:45489486-45489521 log2=0.004 spread=0.005 rmask=nan
" chr21:45491225-45491314 log2=-0.167 spread=0.247 rmask=nan
" chr21:45492687-45492713 log2=0.218 spread=0.324 rmask=nan
" chr21:45494545-45494571 log2=0.110 spread=0.163 rmask=nan
" chr21:45504416-45504556 log2=0.245 spread=0.364 rmask=nan
" chr21:45505134-45505278 log2=0.130 spread=0.193 rmask=nan
" chr21:45505358-45505431 log2=-0.097 spread=0.144 rmask=nan
" chr21:45507561-45507593 log2=-0.021 spread=0.031 rmask=nan
" chr21:45509356-45509601 log2=-0.022 spread=0.032 rmask=nan
" chr21:45510064-45510261 log2=0.192 spread=0.285 rmask=nan
" chr21:45981851-45981947 log2=0.299 spread=0.443 rmask=nan
" chr21:45987610-45987654 log2=0.246 spread=0.365 rmask=nan
" chr21:45990773-45990826 log2=-0.069 spread=0.103 rmask=nan
" chr21:45992010-45992072 log2=0.012 spread=0.018 rmask=nan
" chr21:45992164-45992217 log2=0.100 spread=0.149 rmask=nan
" chr21:45992363-45992398 log2=0.126 spread=0.187 rmask=nan
" chr21:45992748-45992810 log2=0.039 spread=0.058 rmask=nan
" chr21:45997700-45997762 log2=-0.044 spread=0.065 rmask=nan
" chr21:45998121-45998171 log2=0.110 spread=0.163 rmask=nan
" chr21:45998897-45998959 log2=0.148 spread=0.219 rmask=nan
" chr21:45999657-45999692 log2=0.126 spread=0.186 rmask=nan
" chr21:46117874-46117936 log2=-0.039 spread=0.058 rmask=nan
" chr21:46118614-46118676 log2=-0.003 spread=0.004 rmask=nan
" chr21:46119788-46119850 log2=-0.236 spread=0.349 rmask=nan
" chr21:46120515-46120577 log2=-0.174 spread=0.258 rmask=nan
" chr21:46122108-46122158 log2=0.116 spread=0.172 rmask=nan
" chr21:46122496-46122531 log2=0.174 spread=0.259 rmask=nan
" chr21:46124651-46124713 log2=0.082 spread=0.121 rmask=nan
" chr21:46124885-46124920 log2=0.046 spread=0.069 rmask=nan
" chr21:46138508-46138646 log2=0.203 spread=0.301 rmask=nan
" chr21:46145818-46145947 log2=0.231 spread=0.342 rmask=nan
" chr21:46228434-46228599 log2=-0.012 spread=0.018 rmask=nan
" chr21:46284311-46284554 log2=-0.704 spread=1.044 rmask=nan
" chr21:46301999-46302154 log2=0.506 spread=0.750 rmask=nan
" chr21:46314716-46315006 log2=-0.089 spread=0.132 rmask=nan
" chr21:46388742-46388884 log2=0.303 spread=0.449 rmask=nan
" chr21:46398014-46398130 log2=-0.225 spread=0.334 rmask=nan
" chr21:46398235-46398255 log2=-0.144 spread=0.213 rmask=nan
" chr21:46411775-46412067 log2=-0.333 spread=0.493 rmask=nan
" chr21:46459132-46459222 log2=0.279 spread=0.414 rmask=nan
Antitargets: 147 (29.34%) bins failed filters
Wrote ./reference.cnn with 2979 regions
Running 1 samples in 8 processes (that's 8 processes per bam)
Running the CNVkit pipeline on Sig_18_tissue.recalibrated.bam ...
Processing reads in Sig_18_tissue.recalibrated.bam
Time: 39.245 seconds (108586 reads/sec, 63 bins/sec)
Summary: #bins=2478, #reads=4261483, mean=1719.7268, min=2.22, max=13519.28
Percent reads in regions: 34.557 (of 12331635 mapped)
Wrote ./Sig_18_tissue.recalibrated.targetcoverage.cnn with 2478 regions
Processing reads in Sig_18_tissue.recalibrated.bam
Time: 5.716 seconds (245121 reads/sec, 88 bins/sec)
Summary: #bins=501, #reads=1401126, mean=2796.6595, min=0.0, max=223328.08
Percent reads in regions: 11.362 (of 12331635 mapped)
Wrote ./Sig_18_tissue.recalibrated.antitargetcoverage.cnn with 501 regions
Processing target: Sig_18_tissue.recalibrated
Keeping 2129 of 2478 bins
Correcting for GC bias...
Correcting for density bias...
Processing antitarget: Sig_18_tissue.recalibrated
Keeping 354 of 501 bins
Correcting for GC bias...
Correcting for RepeatMasker bias...
Antitargets are 1.39 x more variable than targets
Wrote ./Sig_18_tissue.recalibrated.cnr with 2483 regions
Segmenting ./Sig_18_tissue.recalibrated.cnr ...
Segmenting with method 'cbs', significance threshold 0.0001, in 8 processes
Post-processing ./Sig_18_tissue.recalibrated.cns ...
Wrote ./Sig_18_tissue.recalibrated.cns with 6 regions
Applying filter 'ci'
Filtered by 'ci' from 6 to 5 rows
Calling copy number with thresholds: -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3
Wrote ./Sig_18_tissue.recalibrated.call.cns with 5 regions
Ignoring 354 off-target bins
Significant hits in 122/2129 bins (5.73%)
Wrote ./Sig_18_tissue.recalibrated.bintest.cns with 122 regions
Wrote ./Sig_18_tissue.recalibrated-scatter.png
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?
Wrote ./Sig_18_tissue.recalibrated-diagram.pdf
Matplotlib created a temporary cache directory at /var/tmp/matplotlib-0ihafyxc 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