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/7d/2fbbcfabe22f5701b88dbc56080924/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam
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/HCC1395_BL/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/2fbbcfabe22f5701b88dbc56080924/.command.run
==> STAGING COMPLETE (7 inputs)
Matplotlib created a temporary cache directory at /var/tmp/matplotlib-pjqm3xoi 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 HCC1395_BL.recalibrated.bam
Processing reads in HCC1395_BL.recalibrated.bam
Time: 1.308 seconds (227049 reads/sec, 383 bins/sec)
Summary: #bins=501, #reads=297025, mean=592.8662, min=0.0, max=67819.42666666667
Percent reads in regions: 15.189 (of 1955532 mapped)
Wrote ./HCC1395_BL.recalibrated.antitargetcoverage.cnn with 501 regions
Time: 8.124 seconds (91994 reads/sec, 305 bins/sec)
Summary: #bins=2478, #reads=747388, mean=301.6094, min=0.0, max=2680.8733333333334
Percent reads in regions: 38.219 (of 1955532 mapped)
Wrote ./HCC1395_BL.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 ./HCC1395_BL.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 ./HCC1395_BL.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: 332 (13.4%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)
- chr21:5128214-5128354 log2=0.760 spread=1.127 rmask=nan
" chr21:6119024-6119240 log2=0.052 spread=0.076 rmask=nan
" chr21:6121144-6121519 log2=0.088 spread=0.130 rmask=nan
" chr21:6447736-6447777 log2=-0.341 spread=0.506 rmask=nan
" chr21:6456881-6456950 log2=-2.225 spread=3.299 rmask=nan
" chr21:6484769-6484916 log2=0.801 spread=1.187 rmask=nan
" chr21:6487107-6487205 log2=-0.848 spread=1.257 rmask=nan
" chr21:6495993-6496080 log2=0.993 spread=1.472 rmask=nan
" chr21:10413740-10413754 log2=0.863 spread=1.280 rmask=nan
" chr21:10454134-10454296 log2=0.904 spread=1.341 rmask=nan
" chr21:10462836-10462886 log2=1.005 spread=1.491 rmask=nan
" chr21:10538724-10538734 log2=0.629 spread=0.933 rmask=nan
" chr21:10552657-10552716 log2=0.920 spread=1.363 rmask=nan
" chr21:10559494-10559544 log2=0.859 spread=1.273 rmask=nan
" chr21:10592293-10592373 log2=0.747 spread=1.107 rmask=nan
" chr21:10602058-10602150 log2=0.709 spread=1.051 rmask=nan
" chr21:13610229-13610488 log2=-1.137 spread=1.685 rmask=nan
" chr21:13610489-13610749 log2=-0.781 spread=1.158 rmask=nan
" chr21:13615397-13615570 log2=-0.992 spread=1.471 rmask=nan
" chr21:13622805-13622875 log2=-0.444 spread=0.659 rmask=nan
" chr21:14592622-14592639 log2=-0.179 spread=0.266 rmask=nan
" chr21:14612876-14612913 log2=0.254 spread=0.376 rmask=nan
" chr21:14615976-14616016 log2=0.244 spread=0.362 rmask=nan
" chr21:15811137-15811210 log2=-0.702 spread=1.040 rmask=nan
" chr21:18245224-18245302 log2=-0.091 spread=0.135 rmask=nan
" chr21:18359757-18359863 log2=0.091 spread=0.134 rmask=nan
" chr21:18397879-18397946 log2=0.430 spread=0.637 rmask=nan
" chr21:21385604-21385608 log2=0.359 spread=0.532 rmask=nan
" chr21:25639822-25639888 log2=-0.164 spread=0.244 rmask=nan
" chr21:25714640-25714672 log2=-0.012 spread=0.017 rmask=nan
" chr21:26170564-26170620 log2=0.014 spread=0.020 rmask=nan
" chr21:26844225-26844467 log2=-0.307 spread=0.455 rmask=nan
" chr21:26844711-26844954 log2=0.044 spread=0.065 rmask=nan
" chr21:26965564-26965839 log2=-0.285 spread=0.423 rmask=nan
" chr21:26966116-26966391 log2=-0.084 spread=0.125 rmask=nan
" chr21:29040609-29040687 log2=0.010 spread=0.014 rmask=nan
" chr21:29091501-29091576 log2=-1.983 spread=2.940 rmask=nan
" chr21:31559261-31559595 log2=-0.391 spread=0.579 rmask=nan
" chr21:31705423-31705467 log2=0.126 spread=0.186 rmask=nan
" chr21:31873675-31873935 log2=-0.133 spread=0.197 rmask=nan
" chr21:32392769-32392910 log2=0.015 spread=0.022 rmask=nan
" chr21:32645646-32645789 log2=0.178 spread=0.263 rmask=nan
" chr21:32769814-32769942 log2=0.032 spread=0.048 rmask=nan
" chr21:32771326-32771668 log2=-0.095 spread=0.141 rmask=nan
" chr21:33027349-33027591 log2=-0.381 spread=0.565 rmask=nan
" chr21:33027592-33027834 log2=-0.350 spread=0.520 rmask=nan
" chr21:33070247-33070518 log2=-0.034 spread=0.050 rmask=nan
" chr21:33070519-33070790 log2=-0.631 spread=0.935 rmask=nan
" chr21:33070791-33071062 log2=-0.419 spread=0.621 rmask=nan
" chr21:33403544-33403616 log2=-0.167 spread=0.247 rmask=nan
" chr21:33557546-33557551 log2=0.339 spread=0.502 rmask=nan
" chr21:33588321-33588641 log2=-0.003 spread=0.004 rmask=nan
" chr21:33915728-33915763 log2=0.156 spread=0.231 rmask=nan
" chr21:34614760-34615011 log2=0.060 spread=0.089 rmask=nan
" chr21:34669389-34669662 log2=-0.325 spread=0.482 rmask=nan
" chr21:34669663-34669937 log2=-0.220 spread=0.326 rmask=nan
" chr21:34669938-34670212 log2=-0.011 spread=0.017 rmask=nan
" chr21:34670213-34670487 log2=-0.362 spread=0.536 rmask=nan
" chr21:34670488-34670762 log2=-0.320 spread=0.474 rmask=nan
" chr21:34782802-34782921 log2=0.683 spread=1.013 rmask=nan
" chr21:34787802-34788068 log2=0.982 spread=1.456 rmask=nan
" chr21:34788069-34788336 log2=0.995 spread=1.475 rmask=nan
" chr21:34788337-34788604 log2=0.977 spread=1.448 rmask=nan
" chr21:34788605-34788872 log2=1.012 spread=1.500 rmask=nan
" chr21:34788873-34789139 log2=1.009 spread=1.496 rmask=nan
" chr21:34789140-34789407 log2=1.068 spread=1.583 rmask=nan
" chr21:34789408-34789675 log2=1.109 spread=1.644 rmask=nan
" chr21:34789676-34789943 log2=1.065 spread=1.578 rmask=nan
" chr21:34789944-34790211 log2=0.931 spread=1.381 rmask=nan
" chr21:34790212-34790478 log2=0.975 spread=1.445 rmask=nan
" chr21:34790479-34790746 log2=0.731 spread=1.083 rmask=nan
" chr21:34790747-34791014 log2=0.720 spread=1.068 rmask=nan
" chr21:34791015-34791282 log2=0.940 spread=1.394 rmask=nan
" chr21:34791283-34791549 log2=0.795 spread=1.179 rmask=nan
" chr21:34791550-34791817 log2=0.977 spread=1.448 rmask=nan
" chr21:34791818-34792085 log2=0.467 spread=0.693 rmask=nan
" chr21:34792086-34792353 log2=0.340 spread=0.504 rmask=nan
" chr21:34792354-34792621 log2=0.808 spread=1.197 rmask=nan
" chr21:34799295-34799464 log2=0.699 spread=1.037 rmask=nan
" chr21:34821280-34821487 log2=1.245 spread=1.846 rmask=nan
" chr21:34821488-34821696 log2=0.874 spread=1.296 rmask=nan
" chr21:34834409-34834601 log2=0.870 spread=1.289 rmask=nan
" chr21:34859439-34859439 log2=1.097 spread=1.627 rmask=nan
" chr21:34859473-34859578 log2=0.682 spread=1.012 rmask=nan
" chr21:34886841-34887104 log2=0.883 spread=1.309 rmask=nan
" chr21:34887369-34887632 log2=0.960 spread=1.423 rmask=nan
" chr21:34887633-34887897 log2=0.979 spread=1.451 rmask=nan
" chr21:34887898-34888161 log2=0.899 spread=1.333 rmask=nan
" chr21:34888162-34888425 log2=0.872 spread=1.293 rmask=nan
" chr21:34888426-34888690 log2=1.011 spread=1.500 rmask=nan
" chr21:35048842-35049092 log2=1.033 spread=1.532 rmask=nan
" chr21:35049093-35049344 log2=1.263 spread=1.872 rmask=nan
" chr21:36041807-36041888 log2=0.360 spread=0.534 rmask=nan
" chr21:36320265-36320303 log2=0.054 spread=0.079 rmask=nan
" chr21:36709168-36709250 log2=0.017 spread=0.025 rmask=nan
" chr21:36747665-36747878 log2=-0.425 spread=0.630 rmask=nan
" chr21:36747879-36748092 log2=-0.514 spread=0.761 rmask=nan
" chr21:36966444-36966638 log2=-0.108 spread=0.160 rmask=nan
" chr21:37006773-37006876 log2=-0.007 spread=0.010 rmask=nan
" chr21:37073429-37073483 log2=-0.139 spread=0.206 rmask=nan
" chr21:37090233-37090286 log2=-0.025 spread=0.038 rmask=nan
" chr21:38121128-38121255 log2=-0.857 spread=1.271 rmask=nan
" chr21:38380028-38380286 log2=1.106 spread=1.640 rmask=nan
" chr21:38380287-38380546 log2=0.732 spread=1.085 rmask=nan
" chr21:38380547-38380806 log2=1.069 spread=1.584 rmask=nan
" chr21:38380807-38381065 log2=0.874 spread=1.296 rmask=nan
" chr21:38381066-38381325 log2=0.827 spread=1.226 rmask=nan
" chr21:38381326-38381585 log2=0.782 spread=1.159 rmask=nan
" chr21:38381586-38381845 log2=0.878 spread=1.301 rmask=nan
" chr21:38381846-38382104 log2=0.901 spread=1.336 rmask=nan
" chr21:38382105-38382364 log2=0.896 spread=1.329 rmask=nan
" chr21:38382365-38382624 log2=1.101 spread=1.633 rmask=nan
" chr21:38382885-38383143 log2=0.869 spread=1.288 rmask=nan
" chr21:38383144-38383403 log2=0.871 spread=1.291 rmask=nan
" chr21:38383404-38383663 log2=0.884 spread=1.311 rmask=nan
" chr21:38383664-38383923 log2=0.882 spread=1.308 rmask=nan
" chr21:38390995-38391042 log2=0.736 spread=1.090 rmask=nan
" chr21:38423410-38423561 log2=0.758 spread=1.124 rmask=nan
" chr21:38660523-38660667 log2=0.793 spread=1.176 rmask=nan
" chr21:38805971-38806120 log2=0.169 spread=0.251 rmask=nan
" chr21:39313443-39313491 log2=0.025 spread=0.038 rmask=nan
" chr21:39380523-39380552 log2=0.058 spread=0.086 rmask=nan
" chr21:39788167-39788188 log2=0.358 spread=0.530 rmask=nan
" chr21:40846619-40846661 log2=-0.830 spread=1.230 rmask=nan
" chr21:41168264-41168575 log2=0.029 spread=0.043 rmask=nan
" chr21:41464388-41464639 log2=0.953 spread=1.412 rmask=nan
" chr21:41464640-41464891 log2=1.043 spread=1.547 rmask=nan
" chr21:41464892-41465143 log2=0.998 spread=1.479 rmask=nan
" chr21:41465144-41465396 log2=0.848 spread=1.257 rmask=nan
" chr21:41465397-41465648 log2=0.676 spread=1.003 rmask=nan
" chr21:41465649-41465900 log2=0.945 spread=1.402 rmask=nan
" chr21:41465901-41466153 log2=1.030 spread=1.527 rmask=nan
" chr21:41471806-41471981 log2=0.830 spread=1.230 rmask=nan
" chr21:41476577-41476620 log2=0.739 spread=1.096 rmask=nan
" chr21:41480933-41481212 log2=0.939 spread=1.393 rmask=nan
" chr21:41481213-41481492 log2=0.848 spread=1.257 rmask=nan
" chr21:41481493-41481772 log2=1.041 spread=1.544 rmask=nan
" chr21:41482133-41482432 log2=0.962 spread=1.427 rmask=nan
" chr21:41482433-41482732 log2=1.087 spread=1.612 rmask=nan
" chr21:41482733-41483032 log2=0.839 spread=1.244 rmask=nan
" chr21:41483033-41483332 log2=0.976 spread=1.447 rmask=nan
" chr21:41483573-41483812 log2=1.062 spread=1.575 rmask=nan
" chr21:41484173-41484472 log2=1.128 spread=1.672 rmask=nan
" chr21:41484473-41484772 log2=1.135 spread=1.683 rmask=nan
" chr21:41484773-41485072 log2=0.842 spread=1.249 rmask=nan
" chr21:41485073-41485372 log2=0.989 spread=1.466 rmask=nan
" chr21:41485733-41486032 log2=0.850 spread=1.260 rmask=nan
" chr21:41486033-41486332 log2=1.027 spread=1.522 rmask=nan
" chr21:41486573-41486872 log2=0.935 spread=1.386 rmask=nan
" chr21:41486873-41487172 log2=0.964 spread=1.429 rmask=nan
" chr21:41487173-41487472 log2=0.911 spread=1.351 rmask=nan
" chr21:41487473-41487772 log2=0.994 spread=1.474 rmask=nan
" chr21:41488133-41488372 log2=0.915 spread=1.356 rmask=nan
" chr21:41488373-41488612 log2=0.843 spread=1.249 rmask=nan
" chr21:41488973-41489252 log2=0.900 spread=1.334 rmask=nan
" chr21:41489253-41489532 log2=0.736 spread=1.091 rmask=nan
" chr21:41489533-41489812 log2=0.918 spread=1.361 rmask=nan
" chr21:41490173-41490412 log2=1.210 spread=1.793 rmask=nan
" chr21:41490413-41490652 log2=0.950 spread=1.408 rmask=nan
" chr21:41490893-41491132 log2=1.035 spread=1.534 rmask=nan
" chr21:41491493-41491732 log2=1.053 spread=1.562 rmask=nan
" chr21:41491733-41491972 log2=0.991 spread=1.470 rmask=nan
" chr21:41492213-41492492 log2=1.055 spread=1.563 rmask=nan
" chr21:41492493-41492772 log2=0.889 spread=1.318 rmask=nan
" chr21:41492773-41493052 log2=0.859 spread=1.274 rmask=nan
" chr21:41493053-41493332 log2=0.710 spread=1.053 rmask=nan
" chr21:41493333-41493612 log2=0.743 spread=1.101 rmask=nan
" chr21:41493613-41493892 log2=0.990 spread=1.467 rmask=nan
" chr21:41493893-41494172 log2=0.940 spread=1.393 rmask=nan
" chr21:41494453-41494732 log2=0.926 spread=1.373 rmask=nan
" chr21:41495093-41495332 log2=0.840 spread=1.245 rmask=nan
" chr21:41495693-41495962 log2=0.941 spread=1.394 rmask=nan
" chr21:41495963-41496232 log2=0.948 spread=1.406 rmask=nan
" chr21:41496233-41496502 log2=0.886 spread=1.314 rmask=nan
" chr21:41496503-41496772 log2=0.957 spread=1.418 rmask=nan
" chr21:41497133-41497394 log2=0.938 spread=1.390 rmask=nan
" chr21:41497395-41497657 log2=0.954 spread=1.414 rmask=nan
" chr21:41497658-41497919 log2=0.807 spread=1.196 rmask=nan
" chr21:41497920-41498182 log2=0.804 spread=1.193 rmask=nan
" chr21:41498183-41498444 log2=1.079 spread=1.600 rmask=nan
" chr21:41498445-41498707 log2=0.868 spread=1.287 rmask=nan
" chr21:41498708-41498969 log2=0.793 spread=1.176 rmask=nan
" chr21:41498970-41499232 log2=0.765 spread=1.134 rmask=nan
" chr21:41499233-41499494 log2=0.999 spread=1.481 rmask=nan
" chr21:41499495-41499757 log2=0.900 spread=1.335 rmask=nan
" chr21:41499758-41500019 log2=0.883 spread=1.310 rmask=nan
" chr21:41500020-41500282 log2=0.896 spread=1.328 rmask=nan
" chr21:41500283-41500544 log2=1.010 spread=1.498 rmask=nan
" chr21:41500545-41500807 log2=1.124 spread=1.666 rmask=nan
" chr21:41500808-41501069 log2=0.954 spread=1.414 rmask=nan
" chr21:41501070-41501332 log2=1.052 spread=1.560 rmask=nan
" chr21:41501693-41501962 log2=0.983 spread=1.458 rmask=nan
" chr21:41501963-41502232 log2=0.795 spread=1.179 rmask=nan
" chr21:41502233-41502502 log2=0.899 spread=1.332 rmask=nan
" chr21:41502503-41502772 log2=1.045 spread=1.549 rmask=nan
" chr21:41502773-41503042 log2=1.191 spread=1.766 rmask=nan
" chr21:41503043-41503312 log2=0.978 spread=1.451 rmask=nan
" chr21:41503313-41503582 log2=0.901 spread=1.336 rmask=nan
" chr21:41503583-41503852 log2=1.089 spread=1.614 rmask=nan
" chr21:41503853-41504122 log2=0.896 spread=1.328 rmask=nan
" chr21:41504123-41504392 log2=0.928 spread=1.376 rmask=nan
" chr21:41504393-41504662 log2=1.100 spread=1.632 rmask=nan
" chr21:41504663-41504932 log2=0.861 spread=1.276 rmask=nan
" chr21:41504933-41505202 log2=0.959 spread=1.422 rmask=nan
" chr21:41505203-41505472 log2=1.185 spread=1.757 rmask=nan
" chr21:41505473-41505742 log2=0.910 spread=1.349 rmask=nan
" chr21:41505743-41506012 log2=0.894 spread=1.326 rmask=nan
" chr21:41506013-41506282 log2=0.875 spread=1.297 rmask=nan
" chr21:41506283-41506552 log2=0.736 spread=1.091 rmask=nan
" chr21:41506553-41506822 log2=0.850 spread=1.260 rmask=nan
" chr21:41506823-41507092 log2=0.705 spread=1.046 rmask=nan
" chr21:41507093-41507362 log2=0.803 spread=1.191 rmask=nan
" chr21:41507363-41507632 log2=0.685 spread=1.016 rmask=nan
" chr21:41507633-41507902 log2=0.809 spread=1.199 rmask=nan
" chr21:41507903-41508172 log2=0.824 spread=1.222 rmask=nan
" chr21:41508173-41508442 log2=0.756 spread=1.120 rmask=nan
" chr21:41508443-41508712 log2=0.799 spread=1.185 rmask=nan
" chr21:41508713-41508982 log2=0.752 spread=1.115 rmask=nan
" chr21:41508983-41509252 log2=1.016 spread=1.506 rmask=nan
" chr21:41509613-41509852 log2=1.056 spread=1.565 rmask=nan
" chr21:41509853-41510092 log2=0.762 spread=1.130 rmask=nan
" chr21:41510093-41510332 log2=0.882 spread=1.307 rmask=nan
" chr21:41510453-41510692 log2=0.702 spread=1.041 rmask=nan
" chr21:41510693-41510932 log2=1.010 spread=1.498 rmask=nan
" chr21:41511173-41511406 log2=1.141 spread=1.692 rmask=nan
" chr21:41511407-41511640 log2=0.916 spread=1.358 rmask=nan
" chr21:41511641-41511874 log2=0.732 spread=1.086 rmask=nan
" chr21:41511875-41512108 log2=1.106 spread=1.639 rmask=nan
" chr21:41529974-41530218 log2=1.129 spread=1.674 rmask=nan
" chr21:41530986-41531116 log2=1.155 spread=1.713 rmask=nan
" chr21:41878695-41878860 log2=-0.272 spread=0.403 rmask=nan
" chr21:41878996-41879140 log2=-0.222 spread=0.330 rmask=nan
" chr21:41953370-41953648 log2=-0.036 spread=0.053 rmask=nan
" chr21:42111157-42111433 log2=-0.015 spread=0.023 rmask=nan
" chr21:42855682-42855780 log2=-0.174 spread=0.258 rmask=nan
" chr21:43067778-43067778 log2=0.455 spread=0.675 rmask=nan
" chr21:43092957-43093249 log2=0.675 spread=1.001 rmask=nan
" chr21:43094655-43094788 log2=0.715 spread=1.061 rmask=nan
" chr21:43095438-43095536 log2=0.676 spread=1.002 rmask=nan
" chr21:43104315-43104548 log2=0.919 spread=1.362 rmask=nan
" chr21:43104549-43104783 log2=0.788 spread=1.168 rmask=nan
" chr21:43104784-43105017 log2=0.696 spread=1.031 rmask=nan
" chr21:43105018-43105252 log2=1.079 spread=1.599 rmask=nan
" chr21:43416742-43417117 log2=-0.037 spread=0.055 rmask=nan
" chr21:43417543-43417774 log2=-0.927 spread=1.375 rmask=nan
" chr21:43419021-43419237 log2=0.084 spread=0.125 rmask=nan
" chr21:43658061-43658096 log2=0.189 spread=0.281 rmask=nan
" chr21:43776204-43776269 log2=0.077 spread=0.114 rmask=nan
" chr21:44108984-44109096 log2=-3.025 spread=4.485 rmask=nan
" chr21:44118763-44118833 log2=-13.550 spread=20.089 rmask=nan
" chr21:44119387-44119523 log2=-1.242 spread=1.841 rmask=nan
" chr21:44120952-44121102 log2=-1.246 spread=1.847 rmask=nan
" chr21:44124580-44124727 log2=-0.850 spread=1.260 rmask=nan
" chr21:44133698-44133838 log2=-0.738 spread=1.094 rmask=nan
" chr21:44218009-44218244 log2=0.755 spread=1.120 rmask=nan
" chr21:44223473-44223752 log2=0.712 spread=1.056 rmask=nan
" chr21:44228476-44228744 log2=0.695 spread=1.030 rmask=nan
" chr21:44229552-44229820 log2=-1.387 spread=2.056 rmask=nan
" chr21:44229821-44230089 log2=-0.938 spread=1.390 rmask=nan
" chr21:44233557-44233806 log2=0.734 spread=1.089 rmask=nan
" chr21:44235312-44235562 log2=0.715 spread=1.060 rmask=nan
" chr21:44240804-44241124 log2=0.280 spread=0.415 rmask=nan
" chr21:44241125-44241446 log2=0.363 spread=0.539 rmask=nan
" chr21:44289988-44290068 log2=-0.044 spread=0.065 rmask=nan
" chr21:44292302-44292401 log2=-0.076 spread=0.113 rmask=nan
" chr21:44293789-44293910 log2=-0.161 spread=0.238 rmask=nan
" chr21:44294401-44294503 log2=-0.074 spread=0.109 rmask=nan
" chr21:44300106-44300190 log2=0.025 spread=0.037 rmask=nan
" chr21:44424852-44424939 log2=-0.072 spread=0.106 rmask=nan
" chr21:44550947-44551202 log2=-0.685 spread=1.016 rmask=nan
" chr21:44573759-44573999 log2=0.715 spread=1.059 rmask=nan
" chr21:44574241-44574481 log2=-0.835 spread=1.238 rmask=nan
" chr21:44574482-44574722 log2=-1.006 spread=1.491 rmask=nan
" chr21:44580307-44580578 log2=-0.177 spread=0.262 rmask=nan
" chr21:44591936-44592209 log2=-0.730 spread=1.082 rmask=nan
" chr21:44600900-44601177 log2=-0.813 spread=1.205 rmask=nan
" chr21:44601178-44601455 log2=-0.770 spread=1.142 rmask=nan
" chr21:44637670-44637921 log2=-0.724 spread=1.073 rmask=nan
" chr21:44646758-44647056 log2=-0.712 spread=1.056 rmask=nan
" chr21:44697694-44697939 log2=-0.192 spread=0.284 rmask=nan
" chr21:44873502-44873616 log2=0.200 spread=0.297 rmask=nan
" chr21:44910725-44910782 log2=0.107 spread=0.159 rmask=nan
" chr21:44940058-44940186 log2=0.297 spread=0.440 rmask=nan
" chr21:45405231-45405241 log2=0.145 spread=0.215 rmask=nan
" chr21:45405379-45405473 log2=0.591 spread=0.877 rmask=nan
" chr21:45456611-45456881 log2=-0.113 spread=0.168 rmask=nan
" chr21:45475476-45475535 log2=-0.134 spread=0.199 rmask=nan
" chr21:45477750-45477965 log2=0.060 spread=0.089 rmask=nan
" chr21:45478327-45478353 log2=0.132 spread=0.195 rmask=nan
" chr21:45480700-45480858 log2=-0.017 spread=0.025 rmask=nan
" chr21:45481963-45482025 log2=-0.090 spread=0.134 rmask=nan
" chr21:45486861-45486992 log2=-0.306 spread=0.454 rmask=nan
" chr21:45488418-45488444 log2=-0.018 spread=0.026 rmask=nan
" chr21:45489486-45489521 log2=0.051 spread=0.075 rmask=nan
" chr21:45491225-45491314 log2=-0.080 spread=0.119 rmask=nan
" chr21:45492687-45492713 log2=0.291 spread=0.431 rmask=nan
" chr21:45494545-45494571 log2=0.140 spread=0.207 rmask=nan
" chr21:45504416-45504556 log2=0.218 spread=0.324 rmask=nan
" chr21:45505134-45505278 log2=0.108 spread=0.160 rmask=nan
" chr21:45505358-45505431 log2=-0.102 spread=0.151 rmask=nan
" chr21:45507561-45507593 log2=-0.260 spread=0.385 rmask=nan
" chr21:45509356-45509601 log2=0.065 spread=0.096 rmask=nan
" chr21:45510064-45510261 log2=0.192 spread=0.284 rmask=nan
" chr21:45981851-45981947 log2=0.411 spread=0.610 rmask=nan
" chr21:45987610-45987654 log2=0.218 spread=0.324 rmask=nan
" chr21:45990773-45990826 log2=-0.034 spread=0.051 rmask=nan
" chr21:45992010-45992072 log2=0.054 spread=0.080 rmask=nan
" chr21:45992164-45992217 log2=0.000 spread=0.000 rmask=nan
" chr21:45992363-45992398 log2=0.031 spread=0.046 rmask=nan
" chr21:45992748-45992810 log2=-0.126 spread=0.187 rmask=nan
" chr21:45997700-45997762 log2=0.122 spread=0.180 rmask=nan
" chr21:45998121-45998171 log2=0.205 spread=0.303 rmask=nan
" chr21:45998897-45998959 log2=0.096 spread=0.142 rmask=nan
" chr21:45999657-45999692 log2=-0.045 spread=0.066 rmask=nan
" chr21:46117874-46117936 log2=-0.081 spread=0.121 rmask=nan
" chr21:46118614-46118676 log2=-0.119 spread=0.176 rmask=nan
" chr21:46119788-46119850 log2=-0.153 spread=0.227 rmask=nan
" chr21:46120515-46120577 log2=-0.122 spread=0.181 rmask=nan
" chr21:46122108-46122158 log2=-0.034 spread=0.050 rmask=nan
" chr21:46122496-46122531 log2=0.211 spread=0.312 rmask=nan
" chr21:46124651-46124713 log2=-0.093 spread=0.138 rmask=nan
" chr21:46124885-46124920 log2=0.103 spread=0.153 rmask=nan
" chr21:46138508-46138646 log2=0.272 spread=0.403 rmask=nan
" chr21:46145818-46145947 log2=0.228 spread=0.338 rmask=nan
" chr21:46228434-46228599 log2=0.074 spread=0.110 rmask=nan
" chr21:46301999-46302154 log2=0.468 spread=0.694 rmask=nan
" chr21:46314716-46315006 log2=-0.123 spread=0.182 rmask=nan
" chr21:46388742-46388884 log2=0.221 spread=0.327 rmask=nan
" chr21:46398014-46398130 log2=-0.395 spread=0.586 rmask=nan
" chr21:46398235-46398255 log2=-0.190 spread=0.281 rmask=nan
" chr21:46411775-46412067 log2=-0.303 spread=0.450 rmask=nan
" chr21:46459132-46459222 log2=0.234 spread=0.347 rmask=nan
Antitargets: 144 (28.74%) 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 HCC1395_tumor.recalibrated.bam ...
Processing reads in HCC1395_tumor.recalibrated.bam
Time: 15.194 seconds (118248 reads/sec, 163 bins/sec)
Summary: #bins=2478, #reads=1796667, mean=725.0472, min=2.049586776859504, max=4584.859504132231
Percent reads in regions: 33.544 (of 5356075 mapped)
Wrote ./HCC1395_tumor.recalibrated.targetcoverage.cnn with 2478 regions
Processing reads in HCC1395_tumor.recalibrated.bam
Time: 2.606 seconds (303543 reads/sec, 192 bins/sec)
Summary: #bins=501, #reads=791109, mean=1579.0614, min=0.0, max=189580.78512396695
Percent reads in regions: 14.770 (of 5356075 mapped)
Wrote ./HCC1395_tumor.recalibrated.antitargetcoverage.cnn with 501 regions
Processing target: HCC1395_tumor.recalibrated
Keeping 2146 of 2478 bins
Correcting for GC bias...
Correcting for density bias...
Processing antitarget: HCC1395_tumor.recalibrated
Keeping 357 of 501 bins
Correcting for GC bias...
Correcting for RepeatMasker bias...
Antitargets are 3.07 x more variable than targets
Wrote ./HCC1395_tumor.recalibrated.cnr with 2503 regions
Segmenting ./HCC1395_tumor.recalibrated.cnr ...
Segmenting with method 'cbs', significance threshold 0.0001, in 8 processes
Post-processing ./HCC1395_tumor.recalibrated.cns ...
Wrote ./HCC1395_tumor.recalibrated.cns with 7 regions
Applying filter 'ci'
Filtered by 'ci' from 7 to 5 rows
Calling copy number with thresholds: -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3
Wrote ./HCC1395_tumor.recalibrated.call.cns with 5 regions
Ignoring 357 off-target bins
Significant hits in 75/2146 bins (3.49%)
Wrote ./HCC1395_tumor.recalibrated.bintest.cns with 75 regions
Wrote ./HCC1395_tumor.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 ./HCC1395_tumor.recalibrated-diagram.pdf
Matplotlib created a temporary cache directory at /var/tmp/matplotlib-8lkqlbjd 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