[2019-01-24 12:11:17.291] [jointLog] [info] parsing read library format [2019-01-24 12:11:17.291] [jointLog] [info] There is 1 library. [2019-01-24 12:11:17.353] [jointLog] [info] Loading Quasi index [2019-01-24 12:11:17.354] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:11:20.133] [jointLog] [info] done [2019-01-24 12:11:20.133] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:12:42.491] [fileLog] [info] At end of round 0 ================== Observed 34532223 total fragments (34532223 in most recent round) [2019-01-24 12:12:42.491] [jointLog] [info] Computed 68550 rich equivalence classes for further processing [2019-01-24 12:12:42.491] [jointLog] [info] Counted 17762650 total reads in the equivalence classes [2019-01-24 12:12:42.500] [jointLog] [warning] 0.0188954% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 12:12:42.500] [jointLog] [info] Mapping rate = 51.4379% [2019-01-24 12:12:42.500] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:12:42.500] [jointLog] [info] Starting optimizer [2019-01-24 12:12:42.543] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:12:42.544] [jointLog] [info] iteration = 0 | max rel diff. = 244.633 [2019-01-24 12:12:42.677] [jointLog] [info] iteration = 100 | max rel diff. = 0.112388 [2019-01-24 12:12:42.807] [jointLog] [info] iteration = 200 | max rel diff. = 0.0542564 [2019-01-24 12:12:42.939] [jointLog] [info] iteration = 300 | max rel diff. = 0.0394619 [2019-01-24 12:12:43.070] [jointLog] [info] iteration = 400 | max rel diff. = 0.0293376 [2019-01-24 12:12:43.201] [jointLog] [info] iteration = 500 | max rel diff. = 0.0236212 [2019-01-24 12:12:43.334] [jointLog] [info] iteration = 600 | max rel diff. = 0.0188708 [2019-01-24 12:12:43.465] [jointLog] [info] iteration = 700 | max rel diff. = 0.0184512 [2019-01-24 12:12:43.596] [jointLog] [info] iteration = 800 | max rel diff. = 0.0151061 [2019-01-24 12:12:43.728] [jointLog] [info] iteration = 900 | max rel diff. = 0.0123446 [2019-01-24 12:12:43.861] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0117439 [2019-01-24 12:12:43.993] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107816 [2019-01-24 12:12:44.052] [jointLog] [info] iteration = 1145 | max rel diff. = 0.00949625 [2019-01-24 12:12:44.057] [jointLog] [info] Finished optimizer [2019-01-24 12:12:44.057] [jointLog] [info] writing output [2019-01-24 12:12:44.145] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_03/lib_format_counts.json for details [2019-01-24 12:51:29.421] [jointLog] [info] parsing read library format [2019-01-24 12:51:29.421] [jointLog] [info] There is 1 library. [2019-01-24 12:51:29.483] [jointLog] [info] Loading Quasi index [2019-01-24 12:51:29.483] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:51:32.268] [jointLog] [info] done [2019-01-24 12:51:32.268] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:52:54.855] [fileLog] [info] At end of round 0 ================== Observed 34532223 total fragments (34532223 in most recent round) [2019-01-24 12:52:54.854] [jointLog] [info] Computed 68550 rich equivalence classes for further processing [2019-01-24 12:52:54.854] [jointLog] [info] Counted 17762650 total reads in the equivalence classes [2019-01-24 12:52:54.862] [jointLog] [warning] 0.0188954% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 12:52:54.862] [jointLog] [info] Mapping rate = 51.4379% [2019-01-24 12:52:54.862] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:52:54.862] [jointLog] [info] Starting optimizer [2019-01-24 12:52:54.904] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:52:54.906] [jointLog] [info] iteration = 0 | max rel diff. = 244.633 [2019-01-24 12:52:55.033] [jointLog] [info] iteration = 100 | max rel diff. = 0.112486 [2019-01-24 12:52:55.162] [jointLog] [info] iteration = 200 | max rel diff. = 0.0538464 [2019-01-24 12:52:55.291] [jointLog] [info] iteration = 300 | max rel diff. = 0.0394617 [2019-01-24 12:52:55.420] [jointLog] [info] iteration = 400 | max rel diff. = 0.0283444 [2019-01-24 12:52:55.550] [jointLog] [info] iteration = 500 | max rel diff. = 0.0226101 [2019-01-24 12:52:55.681] [jointLog] [info] iteration = 600 | max rel diff. = 0.0188709 [2019-01-24 12:52:55.810] [jointLog] [info] iteration = 700 | max rel diff. = 0.0183276 [2019-01-24 12:52:55.941] [jointLog] [info] iteration = 800 | max rel diff. = 0.0151061 [2019-01-24 12:52:56.072] [jointLog] [info] iteration = 900 | max rel diff. = 0.0123421 [2019-01-24 12:52:56.204] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0122186 [2019-01-24 12:52:56.337] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107829 [2019-01-24 12:52:56.396] [jointLog] [info] iteration = 1145 | max rel diff. = 0.00949636 [2019-01-24 12:52:56.401] [jointLog] [info] Finished optimizer [2019-01-24 12:52:56.401] [jointLog] [info] writing output [2019-01-24 12:52:56.496] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_03/lib_format_counts.json for details [2019-01-24 20:40:40.281] [jointLog] [info] parsing read library format [2019-01-24 20:40:40.281] [jointLog] [info] There is 1 library. [2019-01-24 20:40:40.343] [jointLog] [info] Loading Quasi index [2019-01-24 20:40:40.343] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:40:43.347] [jointLog] [info] done [2019-01-24 20:40:43.347] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:42:04.904] [fileLog] [info] At end of round 0 ================== Observed 34532223 total fragments (34532223 in most recent round) [2019-01-24 20:42:04.903] [jointLog] [info] Computed 68550 rich equivalence classes for further processing [2019-01-24 20:42:04.903] [jointLog] [info] Counted 17762650 total reads in the equivalence classes [2019-01-24 20:42:04.913] [jointLog] [warning] 0.0188954% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:42:04.913] [jointLog] [info] Mapping rate = 51.4379% [2019-01-24 20:42:04.913] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:42:04.913] [jointLog] [info] Starting optimizer [2019-01-24 20:42:04.952] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:42:04.953] [jointLog] [info] iteration = 0 | max rel diff. = 244.632 [2019-01-24 20:42:05.084] [jointLog] [info] iteration = 100 | max rel diff. = 0.112384 [2019-01-24 20:42:05.214] [jointLog] [info] iteration = 200 | max rel diff. = 0.05385 [2019-01-24 20:42:05.346] [jointLog] [info] iteration = 300 | max rel diff. = 0.0394625 [2019-01-24 20:42:05.478] [jointLog] [info] iteration = 400 | max rel diff. = 0.0283208 [2019-01-24 20:42:05.610] [jointLog] [info] iteration = 500 | max rel diff. = 0.0226103 [2019-01-24 20:42:05.740] [jointLog] [info] iteration = 600 | max rel diff. = 0.0188708 [2019-01-24 20:42:05.870] [jointLog] [info] iteration = 700 | max rel diff. = 0.018486 [2019-01-24 20:42:06.003] [jointLog] [info] iteration = 800 | max rel diff. = 0.0151063 [2019-01-24 20:42:06.135] [jointLog] [info] iteration = 900 | max rel diff. = 0.0134778 [2019-01-24 20:42:06.268] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0117462 [2019-01-24 20:42:06.400] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107751 [2019-01-24 20:42:06.459] [jointLog] [info] iteration = 1145 | max rel diff. = 0.00949558 [2019-01-24 20:42:06.464] [jointLog] [info] Finished optimizer [2019-01-24 20:42:06.464] [jointLog] [info] writing output [2019-01-24 20:42:06.559] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_03/lib_format_counts.json for details