Matplotlib created a temporary cache directory at /var/tmp/matplotlib-11heo7k4 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.recal.bam
Processing reads in HCC1395_BL.recal.bam
Time: 0.297 seconds (0 reads/sec, 1685 bins/sec)
Summary: #bins=501, #reads=0, mean=0.0000, min=0.0, max=0.0
Percent reads in regions: 0.000 (of 1322923 mapped)
Wrote ./HCC1395_BL.antitargetcoverage.cnn with 501 regions
Time: 7.317 seconds (102231 reads/sec, 339 bins/sec)
Summary: #bins=2478, #reads=747989, mean=301.8522, min=0.0, max=2682.0266666666666
Percent reads in regions: 56.541 (of 1322923 mapped)
Wrote ./HCC1395_BL.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.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.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: 331 (13.36%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)
- chr21:5128214-5128354 log2=0.768 spread=1.139 rmask=nan
" chr21:6119024-6119240 log2=0.061 spread=0.090 rmask=nan
" chr21:6121144-6121519 log2=0.069 spread=0.103 rmask=nan
" chr21:6447736-6447777 log2=-0.226 spread=0.335 rmask=nan
" chr21:6456881-6456950 log2=-2.203 spread=3.266 rmask=nan
" chr21:6484769-6484916 log2=0.794 spread=1.177 rmask=nan
" chr21:6487107-6487205 log2=-0.737 spread=1.092 rmask=nan
" chr21:6495993-6496080 log2=1.003 spread=1.487 rmask=nan
" chr21:7467023-7467222 log2=0.692 spread=1.026 rmask=nan
" chr21:10413740-10413754 log2=0.847 spread=1.256 rmask=nan
" chr21:10454134-10454296 log2=0.904 spread=1.340 rmask=nan
" chr21:10462836-10462886 log2=0.995 spread=1.475 rmask=nan
" chr21:10538724-10538734 log2=0.628 spread=0.931 rmask=nan
" chr21:10552657-10552716 log2=0.918 spread=1.362 rmask=nan
" chr21:10559494-10559544 log2=0.875 spread=1.298 rmask=nan
" chr21:10592293-10592373 log2=0.747 spread=1.108 rmask=nan
" chr21:10602058-10602150 log2=0.717 spread=1.063 rmask=nan
" chr21:13610229-13610488 log2=-1.146 spread=1.700 rmask=nan
" chr21:13610489-13610749 log2=-0.771 spread=1.143 rmask=nan
" chr21:13615123-13615237 log2=-0.758 spread=1.123 rmask=nan
" chr21:13615397-13615570 log2=-0.880 spread=1.305 rmask=nan
" chr21:13622805-13622875 log2=-0.564 spread=0.836 rmask=nan
" chr21:14592622-14592639 log2=-0.180 spread=0.267 rmask=nan
" chr21:14612876-14612913 log2=0.253 spread=0.375 rmask=nan
" chr21:14615976-14616016 log2=0.239 spread=0.354 rmask=nan
" chr21:15811137-15811210 log2=-0.696 spread=1.032 rmask=nan
" chr21:18245224-18245302 log2=-0.089 spread=0.133 rmask=nan
" chr21:18359757-18359863 log2=0.093 spread=0.138 rmask=nan
" chr21:18397879-18397946 log2=0.429 spread=0.636 rmask=nan
" chr21:21385604-21385608 log2=0.356 spread=0.528 rmask=nan
" chr21:25639822-25639888 log2=-0.164 spread=0.243 rmask=nan
" chr21:25714640-25714672 log2=-0.006 spread=0.009 rmask=nan
" chr21:26170564-26170620 log2=0.016 spread=0.023 rmask=nan
" chr21:26844225-26844467 log2=-0.298 spread=0.442 rmask=nan
" chr21:26844711-26844954 log2=0.053 spread=0.078 rmask=nan
" chr21:26965564-26965839 log2=-0.283 spread=0.419 rmask=nan
" chr21:26966116-26966391 log2=-0.084 spread=0.125 rmask=nan
" chr21:29040609-29040687 log2=0.011 spread=0.017 rmask=nan
" chr21:29091501-29091576 log2=-1.991 spread=2.952 rmask=nan
" chr21:31559261-31559595 log2=-0.384 spread=0.570 rmask=nan
" chr21:31705423-31705467 log2=0.120 spread=0.178 rmask=nan
" chr21:31873675-31873935 log2=-0.128 spread=0.190 rmask=nan
" chr21:32392769-32392910 log2=0.016 spread=0.023 rmask=nan
" chr21:32645646-32645789 log2=0.180 spread=0.266 rmask=nan
" chr21:32769814-32769942 log2=0.032 spread=0.047 rmask=nan
" chr21:32771326-32771668 log2=-0.095 spread=0.140 rmask=nan
" chr21:33027349-33027591 log2=-0.390 spread=0.577 rmask=nan
" chr21:33027592-33027834 log2=-0.350 spread=0.520 rmask=nan
" chr21:33070247-33070518 log2=-0.037 spread=0.054 rmask=nan
" chr21:33070519-33070790 log2=-0.630 spread=0.934 rmask=nan
" chr21:33070791-33071062 log2=-0.419 spread=0.622 rmask=nan
" chr21:33403544-33403616 log2=-0.156 spread=0.231 rmask=nan
" chr21:33557546-33557551 log2=0.339 spread=0.503 rmask=nan
" chr21:33588321-33588641 log2=-0.003 spread=0.004 rmask=nan
" chr21:33915728-33915763 log2=0.149 spread=0.220 rmask=nan
" chr21:34614760-34615011 log2=0.058 spread=0.086 rmask=nan
" chr21:34669389-34669662 log2=-0.326 spread=0.484 rmask=nan
" chr21:34669663-34669937 log2=-0.226 spread=0.336 rmask=nan
" chr21:34669938-34670212 log2=0.000 spread=0.000 rmask=nan
" chr21:34670213-34670487 log2=-0.365 spread=0.541 rmask=nan
" chr21:34670488-34670762 log2=-0.319 spread=0.474 rmask=nan
" chr21:34782802-34782921 log2=0.692 spread=1.026 rmask=nan
" chr21:34787802-34788068 log2=0.982 spread=1.456 rmask=nan
" chr21:34788069-34788336 log2=0.984 spread=1.460 rmask=nan
" chr21:34788337-34788604 log2=0.977 spread=1.448 rmask=nan
" chr21:34788605-34788872 log2=1.010 spread=1.498 rmask=nan
" chr21:34788873-34789139 log2=1.009 spread=1.496 rmask=nan
" chr21:34789140-34789407 log2=1.064 spread=1.577 rmask=nan
" chr21:34789408-34789675 log2=1.110 spread=1.646 rmask=nan
" chr21:34789676-34789943 log2=1.060 spread=1.572 rmask=nan
" chr21:34789944-34790211 log2=0.934 spread=1.384 rmask=nan
" chr21:34790212-34790478 log2=0.973 spread=1.442 rmask=nan
" chr21:34790479-34790746 log2=0.730 spread=1.083 rmask=nan
" chr21:34790747-34791014 log2=0.720 spread=1.067 rmask=nan
" chr21:34791015-34791282 log2=0.940 spread=1.393 rmask=nan
" chr21:34791283-34791549 log2=0.790 spread=1.171 rmask=nan
" chr21:34791550-34791817 log2=0.983 spread=1.457 rmask=nan
" chr21:34791818-34792085 log2=0.468 spread=0.693 rmask=nan
" chr21:34792086-34792353 log2=0.346 spread=0.513 rmask=nan
" chr21:34792354-34792621 log2=0.809 spread=1.199 rmask=nan
" chr21:34799295-34799464 log2=0.700 spread=1.038 rmask=nan
" chr21:34821280-34821487 log2=1.244 spread=1.845 rmask=nan
" chr21:34821488-34821696 log2=0.873 spread=1.294 rmask=nan
" chr21:34834409-34834601 log2=0.859 spread=1.274 rmask=nan
" chr21:34859439-34859439 log2=1.093 spread=1.620 rmask=nan
" chr21:34859473-34859578 log2=0.685 spread=1.015 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=0.978 spread=1.450 rmask=nan
" chr21:34887898-34888161 log2=0.898 spread=1.331 rmask=nan
" chr21:34888162-34888425 log2=0.871 spread=1.291 rmask=nan
" chr21:34888426-34888690 log2=1.013 spread=1.502 rmask=nan
" chr21:35048842-35049092 log2=1.030 spread=1.527 rmask=nan
" chr21:35049093-35049344 log2=1.264 spread=1.874 rmask=nan
" chr21:36041807-36041888 log2=0.365 spread=0.541 rmask=nan
" chr21:36320265-36320303 log2=0.055 spread=0.081 rmask=nan
" chr21:36709168-36709250 log2=0.021 spread=0.031 rmask=nan
" chr21:36747665-36747878 log2=-0.424 spread=0.629 rmask=nan
" chr21:36747879-36748092 log2=-0.512 spread=0.760 rmask=nan
" chr21:36966444-36966638 log2=-0.103 spread=0.153 rmask=nan
" chr21:37006773-37006876 log2=-0.006 spread=0.009 rmask=nan
" chr21:37073429-37073483 log2=-0.131 spread=0.194 rmask=nan
" chr21:37090233-37090286 log2=-0.024 spread=0.036 rmask=nan
" chr21:38121128-38121255 log2=-0.862 spread=1.278 rmask=nan
" chr21:38380028-38380286 log2=1.105 spread=1.638 rmask=nan
" chr21:38380287-38380546 log2=0.733 spread=1.086 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=0.813 spread=1.205 rmask=nan
" chr21:38381326-38381585 log2=0.782 spread=1.159 rmask=nan
" chr21:38381586-38381845 log2=0.878 spread=1.302 rmask=nan
" chr21:38381846-38382104 log2=0.900 spread=1.335 rmask=nan
" chr21:38382105-38382364 log2=0.889 spread=1.318 rmask=nan
" chr21:38382365-38382624 log2=1.102 spread=1.634 rmask=nan
" chr21:38382885-38383143 log2=0.867 spread=1.286 rmask=nan
" chr21:38383144-38383403 log2=0.864 spread=1.280 rmask=nan
" chr21:38383404-38383663 log2=0.885 spread=1.312 rmask=nan
" chr21:38383664-38383923 log2=0.884 spread=1.310 rmask=nan
" chr21:38390995-38391042 log2=0.735 spread=1.090 rmask=nan
" chr21:38423410-38423561 log2=0.756 spread=1.121 rmask=nan
" chr21:38660523-38660667 log2=0.791 spread=1.173 rmask=nan
" chr21:38805971-38806120 log2=0.168 spread=0.249 rmask=nan
" chr21:39313443-39313491 log2=0.028 spread=0.042 rmask=nan
" chr21:39380523-39380552 log2=0.060 spread=0.089 rmask=nan
" chr21:39788167-39788188 log2=0.362 spread=0.537 rmask=nan
" chr21:40846619-40846661 log2=-0.828 spread=1.228 rmask=nan
" chr21:41168264-41168575 log2=0.037 spread=0.055 rmask=nan
" chr21:41464388-41464639 log2=0.950 spread=1.409 rmask=nan
" chr21:41464640-41464891 log2=1.044 spread=1.548 rmask=nan
" chr21:41464892-41465143 log2=0.996 spread=1.477 rmask=nan
" chr21:41465144-41465396 log2=0.846 spread=1.254 rmask=nan
" chr21:41465397-41465648 log2=0.681 spread=1.010 rmask=nan
" chr21:41465649-41465900 log2=0.944 spread=1.400 rmask=nan
" chr21:41465901-41466153 log2=1.022 spread=1.515 rmask=nan
" chr21:41471806-41471981 log2=0.831 spread=1.232 rmask=nan
" chr21:41476577-41476620 log2=0.742 spread=1.100 rmask=nan
" chr21:41480933-41481212 log2=0.937 spread=1.389 rmask=nan
" chr21:41481213-41481492 log2=0.847 spread=1.256 rmask=nan
" chr21:41481493-41481772 log2=1.032 spread=1.530 rmask=nan
" chr21:41482133-41482432 log2=0.964 spread=1.430 rmask=nan
" chr21:41482433-41482732 log2=1.090 spread=1.615 rmask=nan
" chr21:41482733-41483032 log2=0.839 spread=1.244 rmask=nan
" chr21:41483033-41483332 log2=0.977 spread=1.449 rmask=nan
" chr21:41483573-41483812 log2=1.066 spread=1.581 rmask=nan
" chr21:41484173-41484472 log2=1.134 spread=1.681 rmask=nan
" chr21:41484473-41484772 log2=1.137 spread=1.686 rmask=nan
" chr21:41484773-41485072 log2=0.842 spread=1.248 rmask=nan
" chr21:41485073-41485372 log2=0.989 spread=1.466 rmask=nan
" chr21:41485733-41486032 log2=0.853 spread=1.265 rmask=nan
" chr21:41486033-41486332 log2=1.028 spread=1.524 rmask=nan
" chr21:41486573-41486872 log2=0.938 spread=1.390 rmask=nan
" chr21:41486873-41487172 log2=0.957 spread=1.419 rmask=nan
" chr21:41487173-41487472 log2=0.911 spread=1.351 rmask=nan
" chr21:41487473-41487772 log2=0.995 spread=1.476 rmask=nan
" chr21:41488133-41488372 log2=0.900 spread=1.335 rmask=nan
" chr21:41488373-41488612 log2=0.840 spread=1.245 rmask=nan
" chr21:41488973-41489252 log2=0.899 spread=1.333 rmask=nan
" chr21:41489253-41489532 log2=0.732 spread=1.086 rmask=nan
" chr21:41489533-41489812 log2=0.915 spread=1.357 rmask=nan
" chr21:41490173-41490412 log2=1.210 spread=1.794 rmask=nan
" chr21:41490413-41490652 log2=0.950 spread=1.408 rmask=nan
" chr21:41490893-41491132 log2=1.038 spread=1.539 rmask=nan
" chr21:41491493-41491732 log2=1.050 spread=1.557 rmask=nan
" chr21:41491733-41491972 log2=0.991 spread=1.469 rmask=nan
" chr21:41492213-41492492 log2=1.054 spread=1.562 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=0.707 spread=1.048 rmask=nan
" chr21:41493333-41493612 log2=0.747 spread=1.107 rmask=nan
" chr21:41493613-41493892 log2=0.991 spread=1.470 rmask=nan
" chr21:41493893-41494172 log2=0.932 spread=1.382 rmask=nan
" chr21:41494453-41494732 log2=0.925 spread=1.372 rmask=nan
" chr21:41495093-41495332 log2=0.844 spread=1.251 rmask=nan
" chr21:41495693-41495962 log2=0.941 spread=1.395 rmask=nan
" chr21:41495963-41496232 log2=0.948 spread=1.406 rmask=nan
" chr21:41496233-41496502 log2=0.887 spread=1.314 rmask=nan
" chr21:41496503-41496772 log2=0.957 spread=1.418 rmask=nan
" chr21:41497133-41497394 log2=0.936 spread=1.388 rmask=nan
" chr21:41497395-41497657 log2=0.954 spread=1.415 rmask=nan
" chr21:41497658-41497919 log2=0.789 spread=1.170 rmask=nan
" chr21:41497920-41498182 log2=0.803 spread=1.190 rmask=nan
" chr21:41498183-41498444 log2=1.081 spread=1.602 rmask=nan
" chr21:41498445-41498707 log2=0.862 spread=1.278 rmask=nan
" chr21:41498708-41498969 log2=0.792 spread=1.175 rmask=nan
" chr21:41498970-41499232 log2=0.758 spread=1.124 rmask=nan
" chr21:41499233-41499494 log2=1.001 spread=1.484 rmask=nan
" chr21:41499495-41499757 log2=0.897 spread=1.329 rmask=nan
" chr21:41499758-41500019 log2=0.883 spread=1.310 rmask=nan
" chr21:41500020-41500282 log2=0.887 spread=1.315 rmask=nan
" chr21:41500283-41500544 log2=1.009 spread=1.497 rmask=nan
" chr21:41500545-41500807 log2=1.123 spread=1.666 rmask=nan
" chr21:41500808-41501069 log2=0.953 spread=1.412 rmask=nan
" chr21:41501070-41501332 log2=1.049 spread=1.556 rmask=nan
" chr21:41501693-41501962 log2=0.983 spread=1.457 rmask=nan
" chr21:41501963-41502232 log2=0.790 spread=1.171 rmask=nan
" chr21:41502233-41502502 log2=0.893 spread=1.324 rmask=nan
" chr21:41502503-41502772 log2=1.038 spread=1.538 rmask=nan
" chr21:41502773-41503042 log2=1.192 spread=1.768 rmask=nan
" chr21:41503043-41503312 log2=0.968 spread=1.435 rmask=nan
" chr21:41503313-41503582 log2=0.901 spread=1.336 rmask=nan
" chr21:41503583-41503852 log2=1.078 spread=1.599 rmask=nan
" chr21:41503853-41504122 log2=0.887 spread=1.316 rmask=nan
" chr21:41504123-41504392 log2=0.929 spread=1.377 rmask=nan
" chr21:41504393-41504662 log2=1.097 spread=1.626 rmask=nan
" chr21:41504663-41504932 log2=0.869 spread=1.288 rmask=nan
" chr21:41504933-41505202 log2=0.960 spread=1.423 rmask=nan
" chr21:41505203-41505472 log2=1.186 spread=1.758 rmask=nan
" chr21:41505473-41505742 log2=0.888 spread=1.317 rmask=nan
" chr21:41505743-41506012 log2=0.888 spread=1.317 rmask=nan
" chr21:41506013-41506282 log2=0.871 spread=1.291 rmask=nan
" chr21:41506283-41506552 log2=0.739 spread=1.096 rmask=nan
" chr21:41506553-41506822 log2=0.851 spread=1.261 rmask=nan
" chr21:41506823-41507092 log2=0.705 spread=1.046 rmask=nan
" chr21:41507093-41507362 log2=0.805 spread=1.194 rmask=nan
" chr21:41507363-41507632 log2=0.691 spread=1.024 rmask=nan
" chr21:41507633-41507902 log2=0.809 spread=1.199 rmask=nan
" chr21:41507903-41508172 log2=0.807 spread=1.197 rmask=nan
" chr21:41508173-41508442 log2=0.758 spread=1.123 rmask=nan
" chr21:41508443-41508712 log2=0.793 spread=1.176 rmask=nan
" chr21:41508713-41508982 log2=0.746 spread=1.106 rmask=nan
" chr21:41508983-41509252 log2=1.012 spread=1.501 rmask=nan
" chr21:41509613-41509852 log2=1.054 spread=1.563 rmask=nan
" chr21:41509853-41510092 log2=0.755 spread=1.120 rmask=nan
" chr21:41510093-41510332 log2=0.884 spread=1.311 rmask=nan
" chr21:41510453-41510692 log2=0.703 spread=1.042 rmask=nan
" chr21:41510693-41510932 log2=1.010 spread=1.497 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=1.085 rmask=nan
" chr21:41511875-41512108 log2=1.105 spread=1.639 rmask=nan
" chr21:41529974-41530218 log2=1.132 spread=1.679 rmask=nan
" chr21:41530986-41531116 log2=1.149 spread=1.703 rmask=nan
" chr21:41878695-41878860 log2=-0.272 spread=0.403 rmask=nan
" chr21:41878996-41879140 log2=-0.218 spread=0.323 rmask=nan
" chr21:41953370-41953648 log2=-0.033 spread=0.049 rmask=nan
" chr21:42111157-42111433 log2=-0.015 spread=0.023 rmask=nan
" chr21:42855682-42855780 log2=-0.172 spread=0.255 rmask=nan
" chr21:43067778-43067778 log2=0.431 spread=0.640 rmask=nan
" chr21:43094655-43094788 log2=0.695 spread=1.031 rmask=nan
" chr21:43104315-43104548 log2=0.920 spread=1.364 rmask=nan
" chr21:43104549-43104783 log2=0.781 spread=1.159 rmask=nan
" chr21:43104784-43105017 log2=0.686 spread=1.017 rmask=nan
" chr21:43105018-43105252 log2=1.077 spread=1.597 rmask=nan
" chr21:43416742-43417117 log2=-0.023 spread=0.035 rmask=nan
" chr21:43417543-43417774 log2=-0.985 spread=1.461 rmask=nan
" chr21:43419021-43419237 log2=0.080 spread=0.119 rmask=nan
" chr21:43658061-43658096 log2=0.188 spread=0.279 rmask=nan
" chr21:43776204-43776269 log2=0.078 spread=0.115 rmask=nan
" chr21:44108984-44109096 log2=-2.499 spread=3.705 rmask=nan
" chr21:44118763-44118833 log2=-13.553 spread=20.093 rmask=nan
" chr21:44119387-44119523 log2=-1.262 spread=1.872 rmask=nan
" chr21:44120952-44121102 log2=-1.169 spread=1.733 rmask=nan
" chr21:44124580-44124727 log2=-0.763 spread=1.131 rmask=nan
" chr21:44133698-44133838 log2=-0.757 spread=1.122 rmask=nan
" chr21:44218009-44218244 log2=0.716 spread=1.062 rmask=nan
" chr21:44223473-44223752 log2=0.692 spread=1.027 rmask=nan
" chr21:44229552-44229820 log2=-1.392 spread=2.063 rmask=nan
" chr21:44229821-44230089 log2=-0.934 spread=1.385 rmask=nan
" chr21:44233557-44233806 log2=0.769 spread=1.141 rmask=nan
" chr21:44235312-44235562 log2=0.734 spread=1.088 rmask=nan
" chr21:44240804-44241124 log2=0.291 spread=0.431 rmask=nan
" chr21:44241125-44241446 log2=0.353 spread=0.523 rmask=nan
" chr21:44289988-44290068 log2=-0.038 spread=0.056 rmask=nan
" chr21:44292302-44292401 log2=-0.074 spread=0.109 rmask=nan
" chr21:44293789-44293910 log2=-0.158 spread=0.235 rmask=nan
" chr21:44294401-44294503 log2=-0.071 spread=0.105 rmask=nan
" chr21:44300106-44300190 log2=0.027 spread=0.041 rmask=nan
" chr21:44424852-44424939 log2=-0.069 spread=0.102 rmask=nan
" chr21:44550947-44551202 log2=-0.685 spread=1.015 rmask=nan
" chr21:44573759-44573999 log2=0.718 spread=1.065 rmask=nan
" chr21:44574241-44574481 log2=-0.830 spread=1.231 rmask=nan
" chr21:44574482-44574722 log2=-0.986 spread=1.462 rmask=nan
" chr21:44580307-44580578 log2=-0.173 spread=0.257 rmask=nan
" chr21:44591936-44592209 log2=-0.725 spread=1.075 rmask=nan
" chr21:44600900-44601177 log2=-0.802 spread=1.190 rmask=nan
" chr21:44601178-44601455 log2=-0.774 spread=1.148 rmask=nan
" chr21:44637670-44637921 log2=-0.728 spread=1.080 rmask=nan
" chr21:44646758-44647056 log2=-0.722 spread=1.070 rmask=nan
" chr21:44697694-44697939 log2=-0.188 spread=0.279 rmask=nan
" chr21:44873502-44873616 log2=0.204 spread=0.302 rmask=nan
" chr21:44910725-44910782 log2=0.107 spread=0.159 rmask=nan
" chr21:44940058-44940186 log2=0.293 spread=0.434 rmask=nan
" chr21:45405231-45405241 log2=0.148 spread=0.219 rmask=nan
" chr21:45405379-45405473 log2=0.591 spread=0.877 rmask=nan
" chr21:45456611-45456881 log2=-0.112 spread=0.166 rmask=nan
" chr21:45475476-45475535 log2=-0.132 spread=0.196 rmask=nan
" chr21:45477750-45477965 log2=0.064 spread=0.095 rmask=nan
" chr21:45478327-45478353 log2=0.137 spread=0.202 rmask=nan
" chr21:45480700-45480858 log2=-0.015 spread=0.023 rmask=nan
" chr21:45481963-45482025 log2=-0.086 spread=0.128 rmask=nan
" chr21:45486861-45486992 log2=-0.304 spread=0.451 rmask=nan
" chr21:45488418-45488444 log2=-0.019 spread=0.028 rmask=nan
" chr21:45489486-45489521 log2=0.050 spread=0.074 rmask=nan
" chr21:45491225-45491314 log2=-0.074 spread=0.109 rmask=nan
" chr21:45492687-45492713 log2=0.290 spread=0.430 rmask=nan
" chr21:45494545-45494571 log2=0.139 spread=0.206 rmask=nan
" chr21:45504416-45504556 log2=0.219 spread=0.325 rmask=nan
" chr21:45505134-45505278 log2=0.112 spread=0.165 rmask=nan
" chr21:45505358-45505431 log2=-0.102 spread=0.151 rmask=nan
" chr21:45507561-45507593 log2=-0.254 spread=0.377 rmask=nan
" chr21:45509356-45509601 log2=0.062 spread=0.093 rmask=nan
" chr21:45510064-45510261 log2=0.196 spread=0.290 rmask=nan
" chr21:45981851-45981947 log2=0.414 spread=0.613 rmask=nan
" chr21:45987610-45987654 log2=0.227 spread=0.336 rmask=nan
" chr21:45990773-45990826 log2=-0.035 spread=0.052 rmask=nan
" chr21:45992010-45992072 log2=0.057 spread=0.085 rmask=nan
" chr21:45992164-45992217 log2=0.001 spread=0.002 rmask=nan
" chr21:45992363-45992398 log2=0.029 spread=0.044 rmask=nan
" chr21:45992748-45992810 log2=-0.122 spread=0.181 rmask=nan
" chr21:45997700-45997762 log2=0.129 spread=0.191 rmask=nan
" chr21:45998121-45998171 log2=0.209 spread=0.310 rmask=nan
" chr21:45998897-45998959 log2=0.097 spread=0.144 rmask=nan
" chr21:45999657-45999692 log2=-0.044 spread=0.066 rmask=nan
" chr21:46117874-46117936 log2=-0.079 spread=0.117 rmask=nan
" chr21:46118614-46118676 log2=-0.115 spread=0.171 rmask=nan
" chr21:46119788-46119850 log2=-0.149 spread=0.221 rmask=nan
" chr21:46120515-46120577 log2=-0.118 spread=0.174 rmask=nan
" chr21:46122108-46122158 log2=-0.029 spread=0.043 rmask=nan
" chr21:46122496-46122531 log2=0.211 spread=0.312 rmask=nan
" chr21:46124651-46124713 log2=-0.084 spread=0.125 rmask=nan
" chr21:46124885-46124920 log2=0.102 spread=0.151 rmask=nan
" chr21:46138508-46138646 log2=0.272 spread=0.403 rmask=nan
" chr21:46145818-46145947 log2=0.228 spread=0.337 rmask=nan
" chr21:46228434-46228599 log2=0.073 spread=0.109 rmask=nan
" chr21:46301999-46302154 log2=0.469 spread=0.696 rmask=nan
" chr21:46314716-46315006 log2=-0.122 spread=0.181 rmask=nan
" chr21:46388742-46388884 log2=0.223 spread=0.331 rmask=nan
" chr21:46398014-46398130 log2=-0.394 spread=0.584 rmask=nan
" chr21:46398235-46398255 log2=-0.188 spread=0.279 rmask=nan
" chr21:46411775-46412067 log2=-0.303 spread=0.449 rmask=nan
" chr21:46459132-46459222 log2=0.237 spread=0.351 rmask=nan
Antitargets: 501 (100.0%) 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.recal.bam ...
Processing reads in HCC1395_tumor.recal.bam
Time: 16.662 seconds (87043 reads/sec, 149 bins/sec)
Summary: #bins=2478, #reads=1450328, mean=585.2820, min=0.9, max=3699.8
Percent reads in regions: 40.079 (of 3618678 mapped)
Wrote ./HCC1395_tumor.targetcoverage.cnn with 2478 regions
Processing reads in HCC1395_tumor.recal.bam
Time: 0.625 seconds (0 reads/sec, 802 bins/sec)
Summary: #bins=501, #reads=0, mean=0.0000, min=0.0, max=0.0
Percent reads in regions: 0.000 (of 3618678 mapped)
Wrote ./HCC1395_tumor.antitargetcoverage.cnn with 501 regions
Processing target: HCC1395_tumor
Keeping 2147 of 2478 bins
Correcting for GC bias...
Correcting for density bias...
Processing antitarget: HCC1395_tumor
Keeping 0 of 501 bins
WARNING: most bins have no or very low coverage; check that the right BED file was used
Wrote ./HCC1395_tumor.cnr with 2147 regions
Segmenting ./HCC1395_tumor.cnr ...
Segmenting with method 'cbs', significance threshold 0.0001, in 8 processes
Post-processing ./HCC1395_tumor.cns ...
Wrote ./HCC1395_tumor.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.call.cns with 5 regions
Significant hits in 74/2147 bins (3.45%)
Wrote ./HCC1395_tumor.bintest.cns with 74 regions
Wrote ./HCC1395_tumor-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-diagram.pdf
Matplotlib created a temporary cache directory at /var/tmp/matplotlib-i5dowee1 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