Loading example/example.log +35 −35 Original line number Diff line number Diff line +-----------------------------+ | | | Eagle v2.4 | | December 13, 2017 | | Eagle v2.4.1 | | November 18, 2018 | | Po-Ru Loh | | | +-----------------------------+ Copyright (C) 2015-2017 Harvard University. Copyright (C) 2015-2018 Harvard University. Distributed under the GNU GPLv3+ open source license. Command line options: Loading Loading @@ -56,25 +56,25 @@ Setting --histFactor=1.00 BEGINNING STEP 1 Time for step 1: 0.282519 Time for step 1 MN^2: 0.0201082 Time for step 1: 0.347481 Time for step 1 MN^2: 0.0270685 Making hard calls (time: 0.0164621) Making hard calls (time: 0.0181408) BEGINNING STEP 2 BATCH 1 OF 1 Building hash tables .................................................................. (time: 0.0826769) .................................................................. (time: 0.065696) Phasing samples 1-379 Time for phasing batch: 0.335781 Time for phasing batch: 0.309231 Making hard calls (time: 0.0172811) Making hard calls (time: 0.0192151) Time for step 2: 0.435747 Time for step 2 MN^2: 0.0391194 Time for step 2: 0.394149 Time for step 2 MN^2: 0.0408464 BEGINNING STEP 3 (PBWT ITERS) Loading @@ -87,108 +87,108 @@ BEGINNING PBWT ITER 1 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.13401 Time for phasing batch: 0.977095 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.04853 Time for phasing batch: 0.898498 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.18956 Time for phasing batch: 0.950794 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.1353 Time for phasing batch: 0.937661 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.01419 Time for phasing batch: 0.909736 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.05172 Time for phasing batch: 0.924443 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 0.99322 Time for phasing batch: 0.9072 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 0.99847 Time for phasing batch: 0.926957 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 0.998471 Time for phasing batch: 0.888218 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.05052 Time for phasing batch: 0.90299 Time for PBWT iter 1: 10.6142 Time for PBWT iter 1: 9.22363 BEGINNING PBWT ITER 2 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.76314 Time for phasing batch: 1.49903 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.79145 Time for phasing batch: 1.4698 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.8253 Time for phasing batch: 1.51891 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.54563 Time for phasing batch: 1.45062 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.54299 Time for phasing batch: 1.42069 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.59936 Time for phasing batch: 1.4851 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 1.55847 Time for phasing batch: 1.44716 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 1.51538 Time for phasing batch: 1.49382 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 1.58919 Time for phasing batch: 1.43647 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.64308 Time for phasing batch: 1.46241 Time for PBWT iter 2: 16.3741 Time for PBWT iter 2: 14.6841 Writing .haps.gz and .sample output Time for writing output: 0.281509 Total elapsed time for analysis = 28.1508 sec Time for writing output: 0.221324 Total elapsed time for analysis = 24.9776 sec example/example_ref.log +8 −8 Original line number Diff line number Diff line +-----------------------------+ | | | Eagle v2.4 | | December 13, 2017 | | Eagle v2.4.1 | | November 18, 2018 | | Po-Ru Loh | | | +-----------------------------+ Copyright (C) 2015-2017 Harvard University. Copyright (C) 2015-2018 Harvard University. Distributed under the GNU GPLv3+ open source license. Command line options: Loading @@ -18,7 +18,7 @@ Command line options: --outPrefix=target.phased Setting number of threads to 1 Warning: The index file is older than the data file: ref.bcf.csi [W::hts_idx_load2] The index file is older than the data file: ref.bcf.csi Reference samples: Nref = 169 Target samples: Ntarget = 8 Loading @@ -43,7 +43,7 @@ Average # SNPs per cM: 42 Number of <=(64-SNP, 1cM) segments: 9 Average # SNPs per segment: 47 Time for reading input: 6.18623 sec Time for reading input: 5.09263 sec Fraction of heterozygous genotypes: 0.178114 Typical span of default 100-het history length: 13.44 cM Loading @@ -59,15 +59,15 @@ PHASING ITER 1 OF 1 Phasing target samples ................................................................................ Time for phasing iter 1: 0.144591 Time for phasing iter 1: 0.132139 Writing vcf.gz output to target.phased.vcf.gz [W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String Time for writing output: 0.0239 Total elapsed time for analysis = 6.35535 sec Time for writing output: 0.0356269 Total elapsed time for analysis = 5.26099 sec Mean phase confidence of each target individual: ID PHASE_CONFIDENCE Loading example/example_vcf.log +35 −35 Original line number Diff line number Diff line +-----------------------------+ | | | Eagle v2.4 | | December 13, 2017 | | Eagle v2.4.1 | | November 18, 2018 | | Po-Ru Loh | | | +-----------------------------+ Copyright (C) 2015-2017 Harvard University. Copyright (C) 2015-2018 Harvard University. Distributed under the GNU GPLv3+ open source license. Command line options: Loading Loading @@ -39,25 +39,25 @@ Setting --histFactor=1.00 BEGINNING STEP 1 Time for step 1: 0.267283 Time for step 1 MN^2: 0.0164427 Time for step 1: 0.263286 Time for step 1 MN^2: 0.0227702 Making hard calls (time: 0.0152462) Making hard calls (time: 0.018074) BEGINNING STEP 2 BATCH 1 OF 1 Building hash tables .................................................................. (time: 0.0786691) .................................................................. (time: 0.0552511) Phasing samples 1-379 Time for phasing batch: 0.331454 Time for phasing batch: 0.292423 Making hard calls (time: 0.0164559) Making hard calls (time: 0.0192568) Time for step 2: 0.426586 Time for step 2 MN^2: 0.0375612 Time for step 2: 0.366938 Time for step 2 MN^2: 0.0381578 BEGINNING STEP 3 (PBWT ITERS) Loading @@ -70,108 +70,108 @@ BEGINNING PBWT ITER 1 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.0778 Time for phasing batch: 1.02615 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.0477 Time for phasing batch: 0.964455 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.11441 Time for phasing batch: 0.988999 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.06495 Time for phasing batch: 0.978426 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.07034 Time for phasing batch: 0.935981 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.13122 Time for phasing batch: 0.941438 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 1.07535 Time for phasing batch: 0.935864 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 1.16462 Time for phasing batch: 0.926938 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 1.15337 Time for phasing batch: 0.927558 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.17788 Time for phasing batch: 0.932059 Time for PBWT iter 1: 11.0777 Time for PBWT iter 1: 9.55792 BEGINNING PBWT ITER 2 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.87655 Time for phasing batch: 1.56033 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.6772 Time for phasing batch: 1.49036 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.67862 Time for phasing batch: 1.51976 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.57155 Time for phasing batch: 1.48635 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.57551 Time for phasing batch: 1.43754 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.64418 Time for phasing batch: 1.50166 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 1.60561 Time for phasing batch: 1.48078 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 1.63349 Time for phasing batch: 1.45079 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 1.78741 Time for phasing batch: 1.47995 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.80977 Time for phasing batch: 1.42872 Time for PBWT iter 2: 16.86 Time for PBWT iter 2: 14.8363 Writing vcf.gz output to phased.vcf.gz Time for writing output: 0.204556 Total elapsed time for analysis = 34.7048 sec Time for writing output: 0.176335 Total elapsed time for analysis = 30.3964 sec example/phased.vcf.gz −3 B (196 KiB) File changed.No diff preview for this file type. View original file View changed file example/target.phased.vcf.gz −1 B (20.6 KiB) File changed.No diff preview for this file type. View original file View changed file Loading
example/example.log +35 −35 Original line number Diff line number Diff line +-----------------------------+ | | | Eagle v2.4 | | December 13, 2017 | | Eagle v2.4.1 | | November 18, 2018 | | Po-Ru Loh | | | +-----------------------------+ Copyright (C) 2015-2017 Harvard University. Copyright (C) 2015-2018 Harvard University. Distributed under the GNU GPLv3+ open source license. Command line options: Loading Loading @@ -56,25 +56,25 @@ Setting --histFactor=1.00 BEGINNING STEP 1 Time for step 1: 0.282519 Time for step 1 MN^2: 0.0201082 Time for step 1: 0.347481 Time for step 1 MN^2: 0.0270685 Making hard calls (time: 0.0164621) Making hard calls (time: 0.0181408) BEGINNING STEP 2 BATCH 1 OF 1 Building hash tables .................................................................. (time: 0.0826769) .................................................................. (time: 0.065696) Phasing samples 1-379 Time for phasing batch: 0.335781 Time for phasing batch: 0.309231 Making hard calls (time: 0.0172811) Making hard calls (time: 0.0192151) Time for step 2: 0.435747 Time for step 2 MN^2: 0.0391194 Time for step 2: 0.394149 Time for step 2 MN^2: 0.0408464 BEGINNING STEP 3 (PBWT ITERS) Loading @@ -87,108 +87,108 @@ BEGINNING PBWT ITER 1 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.13401 Time for phasing batch: 0.977095 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.04853 Time for phasing batch: 0.898498 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.18956 Time for phasing batch: 0.950794 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.1353 Time for phasing batch: 0.937661 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.01419 Time for phasing batch: 0.909736 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.05172 Time for phasing batch: 0.924443 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 0.99322 Time for phasing batch: 0.9072 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 0.99847 Time for phasing batch: 0.926957 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 0.998471 Time for phasing batch: 0.888218 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.05052 Time for phasing batch: 0.90299 Time for PBWT iter 1: 10.6142 Time for PBWT iter 1: 9.22363 BEGINNING PBWT ITER 2 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.76314 Time for phasing batch: 1.49903 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.79145 Time for phasing batch: 1.4698 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.8253 Time for phasing batch: 1.51891 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.54563 Time for phasing batch: 1.45062 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.54299 Time for phasing batch: 1.42069 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.59936 Time for phasing batch: 1.4851 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 1.55847 Time for phasing batch: 1.44716 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 1.51538 Time for phasing batch: 1.49382 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 1.58919 Time for phasing batch: 1.43647 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.64308 Time for phasing batch: 1.46241 Time for PBWT iter 2: 16.3741 Time for PBWT iter 2: 14.6841 Writing .haps.gz and .sample output Time for writing output: 0.281509 Total elapsed time for analysis = 28.1508 sec Time for writing output: 0.221324 Total elapsed time for analysis = 24.9776 sec
example/example_ref.log +8 −8 Original line number Diff line number Diff line +-----------------------------+ | | | Eagle v2.4 | | December 13, 2017 | | Eagle v2.4.1 | | November 18, 2018 | | Po-Ru Loh | | | +-----------------------------+ Copyright (C) 2015-2017 Harvard University. Copyright (C) 2015-2018 Harvard University. Distributed under the GNU GPLv3+ open source license. Command line options: Loading @@ -18,7 +18,7 @@ Command line options: --outPrefix=target.phased Setting number of threads to 1 Warning: The index file is older than the data file: ref.bcf.csi [W::hts_idx_load2] The index file is older than the data file: ref.bcf.csi Reference samples: Nref = 169 Target samples: Ntarget = 8 Loading @@ -43,7 +43,7 @@ Average # SNPs per cM: 42 Number of <=(64-SNP, 1cM) segments: 9 Average # SNPs per segment: 47 Time for reading input: 6.18623 sec Time for reading input: 5.09263 sec Fraction of heterozygous genotypes: 0.178114 Typical span of default 100-het history length: 13.44 cM Loading @@ -59,15 +59,15 @@ PHASING ITER 1 OF 1 Phasing target samples ................................................................................ Time for phasing iter 1: 0.144591 Time for phasing iter 1: 0.132139 Writing vcf.gz output to target.phased.vcf.gz [W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String Time for writing output: 0.0239 Total elapsed time for analysis = 6.35535 sec Time for writing output: 0.0356269 Total elapsed time for analysis = 5.26099 sec Mean phase confidence of each target individual: ID PHASE_CONFIDENCE Loading
example/example_vcf.log +35 −35 Original line number Diff line number Diff line +-----------------------------+ | | | Eagle v2.4 | | December 13, 2017 | | Eagle v2.4.1 | | November 18, 2018 | | Po-Ru Loh | | | +-----------------------------+ Copyright (C) 2015-2017 Harvard University. Copyright (C) 2015-2018 Harvard University. Distributed under the GNU GPLv3+ open source license. Command line options: Loading Loading @@ -39,25 +39,25 @@ Setting --histFactor=1.00 BEGINNING STEP 1 Time for step 1: 0.267283 Time for step 1 MN^2: 0.0164427 Time for step 1: 0.263286 Time for step 1 MN^2: 0.0227702 Making hard calls (time: 0.0152462) Making hard calls (time: 0.018074) BEGINNING STEP 2 BATCH 1 OF 1 Building hash tables .................................................................. (time: 0.0786691) .................................................................. (time: 0.0552511) Phasing samples 1-379 Time for phasing batch: 0.331454 Time for phasing batch: 0.292423 Making hard calls (time: 0.0164559) Making hard calls (time: 0.0192568) Time for step 2: 0.426586 Time for step 2 MN^2: 0.0375612 Time for step 2: 0.366938 Time for step 2 MN^2: 0.0381578 BEGINNING STEP 3 (PBWT ITERS) Loading @@ -70,108 +70,108 @@ BEGINNING PBWT ITER 1 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.0778 Time for phasing batch: 1.02615 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.0477 Time for phasing batch: 0.964455 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.11441 Time for phasing batch: 0.988999 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.06495 Time for phasing batch: 0.978426 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.07034 Time for phasing batch: 0.935981 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.13122 Time for phasing batch: 0.941438 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 1.07535 Time for phasing batch: 0.935864 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 1.16462 Time for phasing batch: 0.926938 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 1.15337 Time for phasing batch: 0.927558 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.17788 Time for phasing batch: 0.932059 Time for PBWT iter 1: 11.0777 Time for PBWT iter 1: 9.55792 BEGINNING PBWT ITER 2 BATCH 1 OF 10 Phasing samples 1-37 Time for phasing batch: 1.87655 Time for phasing batch: 1.56033 BATCH 2 OF 10 Phasing samples 38-75 Time for phasing batch: 1.6772 Time for phasing batch: 1.49036 BATCH 3 OF 10 Phasing samples 76-113 Time for phasing batch: 1.67862 Time for phasing batch: 1.51976 BATCH 4 OF 10 Phasing samples 114-151 Time for phasing batch: 1.57155 Time for phasing batch: 1.48635 BATCH 5 OF 10 Phasing samples 152-189 Time for phasing batch: 1.57551 Time for phasing batch: 1.43754 BATCH 6 OF 10 Phasing samples 190-227 Time for phasing batch: 1.64418 Time for phasing batch: 1.50166 BATCH 7 OF 10 Phasing samples 228-265 Time for phasing batch: 1.60561 Time for phasing batch: 1.48078 BATCH 8 OF 10 Phasing samples 266-303 Time for phasing batch: 1.63349 Time for phasing batch: 1.45079 BATCH 9 OF 10 Phasing samples 304-341 Time for phasing batch: 1.78741 Time for phasing batch: 1.47995 BATCH 10 OF 10 Phasing samples 342-379 Time for phasing batch: 1.80977 Time for phasing batch: 1.42872 Time for PBWT iter 2: 16.86 Time for PBWT iter 2: 14.8363 Writing vcf.gz output to phased.vcf.gz Time for writing output: 0.204556 Total elapsed time for analysis = 34.7048 sec Time for writing output: 0.176335 Total elapsed time for analysis = 30.3964 sec
example/phased.vcf.gz −3 B (196 KiB) File changed.No diff preview for this file type. View original file View changed file
example/target.phased.vcf.gz −1 B (20.6 KiB) File changed.No diff preview for this file type. View original file View changed file
