[2019-01-24 12:12:45.577] [jointLog] [info] parsing read library format [2019-01-24 12:12:45.577] [jointLog] [info] There is 1 library. [2019-01-24 12:12:45.639] [jointLog] [info] Loading Quasi index [2019-01-24 12:12:45.639] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:12:48.424] [jointLog] [info] done [2019-01-24 12:12:48.424] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:13:39.854] [jointLog] [info] Computed 65318 rich equivalence classes for further processing [2019-01-24 12:13:39.854] [jointLog] [info] Counted 11317076 total reads in the equivalence classes [2019-01-24 12:13:39.862] [jointLog] [warning] 0.0315555% 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 12:13:39.862] [jointLog] [info] Mapping rate = 50.3052% [2019-01-24 12:13:39.862] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:13:39.862] [jointLog] [info] Starting optimizer [2019-01-24 12:13:39.895] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:13:39.897] [jointLog] [info] iteration = 0 | max rel diff. = 197.278 [2019-01-24 12:13:39.854] [fileLog] [info] At end of round 0 ================== Observed 22496850 total fragments (22496850 in most recent round) [2019-01-24 12:13:40.021] [jointLog] [info] iteration = 100 | max rel diff. = 0.111839 [2019-01-24 12:13:40.151] [jointLog] [info] iteration = 200 | max rel diff. = 0.055273 [2019-01-24 12:13:40.278] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417484 [2019-01-24 12:13:40.404] [jointLog] [info] iteration = 400 | max rel diff. = 0.0277411 [2019-01-24 12:13:40.531] [jointLog] [info] iteration = 500 | max rel diff. = 0.021356 [2019-01-24 12:13:40.659] [jointLog] [info] iteration = 600 | max rel diff. = 0.019444 [2019-01-24 12:13:40.786] [jointLog] [info] iteration = 700 | max rel diff. = 0.0156942 [2019-01-24 12:13:40.915] [jointLog] [info] iteration = 800 | max rel diff. = 0.0140516 [2019-01-24 12:13:41.043] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126679 [2019-01-24 12:13:41.173] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0121164 [2019-01-24 12:13:41.304] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107617 [2019-01-24 12:13:41.432] [jointLog] [info] iteration = 1199 | max rel diff. = 0.00938486 [2019-01-24 12:13:41.437] [jointLog] [info] Finished optimizer [2019-01-24 12:13:41.437] [jointLog] [info] writing output [2019-01-24 12:13:41.529] [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_44_01/lib_format_counts.json for details [2019-01-24 12:52:57.900] [jointLog] [info] parsing read library format [2019-01-24 12:52:57.900] [jointLog] [info] There is 1 library. [2019-01-24 12:52:57.963] [jointLog] [info] Loading Quasi index [2019-01-24 12:52:57.963] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:53:00.704] [jointLog] [info] done [2019-01-24 12:53:00.704] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:53:54.358] [jointLog] [info] Computed 65318 rich equivalence classes for further processing [2019-01-24 12:53:54.358] [jointLog] [info] Counted 11317076 total reads in the equivalence classes [2019-01-24 12:53:54.366] [jointLog] [warning] 0.0315555% 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 12:53:54.366] [jointLog] [info] Mapping rate = 50.3052% [2019-01-24 12:53:54.366] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:53:54.366] [jointLog] [info] Starting optimizer [2019-01-24 12:53:54.476] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:53:54.477] [jointLog] [info] iteration = 0 | max rel diff. = 197.28 [2019-01-24 12:53:54.358] [fileLog] [info] At end of round 0 ================== Observed 22496850 total fragments (22496850 in most recent round) [2019-01-24 12:53:54.600] [jointLog] [info] iteration = 100 | max rel diff. = 0.111755 [2019-01-24 12:53:54.723] [jointLog] [info] iteration = 200 | max rel diff. = 0.0554664 [2019-01-24 12:53:54.845] [jointLog] [info] iteration = 300 | max rel diff. = 0.0418085 [2019-01-24 12:53:54.968] [jointLog] [info] iteration = 400 | max rel diff. = 0.0277522 [2019-01-24 12:53:55.092] [jointLog] [info] iteration = 500 | max rel diff. = 0.0213555 [2019-01-24 12:53:55.220] [jointLog] [info] iteration = 600 | max rel diff. = 0.0222918 [2019-01-24 12:53:55.344] [jointLog] [info] iteration = 700 | max rel diff. = 0.0159747 [2019-01-24 12:53:55.471] [jointLog] [info] iteration = 800 | max rel diff. = 0.0140513 [2019-01-24 12:53:55.595] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126676 [2019-01-24 12:53:55.719] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110665 [2019-01-24 12:53:55.844] [jointLog] [info] iteration = 1100 | max rel diff. = 0.010764 [2019-01-24 12:53:55.966] [jointLog] [info] iteration = 1198 | max rel diff. = 0.00966113 [2019-01-24 12:53:55.971] [jointLog] [info] Finished optimizer [2019-01-24 12:53:55.971] [jointLog] [info] writing output [2019-01-24 12:53:56.064] [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_44_01/lib_format_counts.json for details [2019-01-24 20:42:07.963] [jointLog] [info] parsing read library format [2019-01-24 20:42:07.963] [jointLog] [info] There is 1 library. [2019-01-24 20:42:08.024] [jointLog] [info] Loading Quasi index [2019-01-24 20:42:08.024] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:42:10.751] [jointLog] [info] done [2019-01-24 20:42:10.751] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:43:04.583] [fileLog] [info] At end of round 0 ================== Observed 22496850 total fragments (22496850 in most recent round) [2019-01-24 20:43:04.582] [jointLog] [info] Computed 65318 rich equivalence classes for further processing [2019-01-24 20:43:04.582] [jointLog] [info] Counted 11317076 total reads in the equivalence classes [2019-01-24 20:43:04.590] [jointLog] [warning] 0.0315555% 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 20:43:04.591] [jointLog] [info] Mapping rate = 50.3052% [2019-01-24 20:43:04.591] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:43:04.591] [jointLog] [info] Starting optimizer [2019-01-24 20:43:04.628] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:43:04.629] [jointLog] [info] iteration = 0 | max rel diff. = 197.278 [2019-01-24 20:43:04.753] [jointLog] [info] iteration = 100 | max rel diff. = 0.111824 [2019-01-24 20:43:04.876] [jointLog] [info] iteration = 200 | max rel diff. = 0.0552807 [2019-01-24 20:43:04.999] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417485 [2019-01-24 20:43:05.125] [jointLog] [info] iteration = 400 | max rel diff. = 0.0278165 [2019-01-24 20:43:05.250] [jointLog] [info] iteration = 500 | max rel diff. = 0.021356 [2019-01-24 20:43:05.378] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192814 [2019-01-24 20:43:05.504] [jointLog] [info] iteration = 700 | max rel diff. = 0.015984 [2019-01-24 20:43:05.630] [jointLog] [info] iteration = 800 | max rel diff. = 0.0140516 [2019-01-24 20:43:05.755] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126681 [2019-01-24 20:43:05.882] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110663 [2019-01-24 20:43:06.010] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107412 [2019-01-24 20:43:06.138] [jointLog] [info] iteration = 1200 | max rel diff. = 0.010121 [2019-01-24 20:43:06.144] [jointLog] [info] iteration = 1206 | max rel diff. = 0.00938457 [2019-01-24 20:43:06.149] [jointLog] [info] Finished optimizer [2019-01-24 20:43:06.149] [jointLog] [info] writing output [2019-01-24 20:43:06.244] [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_44_01/lib_format_counts.json for details