[2019-01-24 12:02:28.261] [jointLog] [info] parsing read library format [2019-01-24 12:02:28.261] [jointLog] [info] There is 1 library. [2019-01-24 12:02:28.322] [jointLog] [info] Loading Quasi index [2019-01-24 12:02:28.322] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:02:31.332] [jointLog] [info] done [2019-01-24 12:02:31.332] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:03:40.592] [fileLog] [info] At end of round 0 ================== Observed 28323045 total fragments (28323045 in most recent round) [2019-01-24 12:03:40.592] [jointLog] [info] Computed 65041 rich equivalence classes for further processing [2019-01-24 12:03:40.592] [jointLog] [info] Counted 15162807 total reads in the equivalence classes [2019-01-24 12:03:40.600] [jointLog] [warning] 0.0118102% 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 12:03:40.600] [jointLog] [info] Mapping rate = 53.5352% [2019-01-24 12:03:40.600] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:03:40.600] [jointLog] [info] Starting optimizer [2019-01-24 12:03:40.643] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:03:40.645] [jointLog] [info] iteration = 0 | max rel diff. = 223.914 [2019-01-24 12:03:40.768] [jointLog] [info] iteration = 100 | max rel diff. = 0.11317 [2019-01-24 12:03:40.891] [jointLog] [info] iteration = 200 | max rel diff. = 0.0566746 [2019-01-24 12:03:41.016] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433005 [2019-01-24 12:03:41.142] [jointLog] [info] iteration = 400 | max rel diff. = 0.0277325 [2019-01-24 12:03:41.266] [jointLog] [info] iteration = 500 | max rel diff. = 0.0228646 [2019-01-24 12:03:41.392] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192937 [2019-01-24 12:03:41.518] [jointLog] [info] iteration = 700 | max rel diff. = 0.0154803 [2019-01-24 12:03:41.644] [jointLog] [info] iteration = 800 | max rel diff. = 0.0150453 [2019-01-24 12:03:41.772] [jointLog] [info] iteration = 900 | max rel diff. = 0.0124748 [2019-01-24 12:03:41.901] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0122231 [2019-01-24 12:03:42.027] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0119931 [2019-01-24 12:03:42.155] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101907 [2019-01-24 12:03:42.237] [jointLog] [info] iteration = 1263 | max rel diff. = 0.00891937 [2019-01-24 12:03:42.242] [jointLog] [info] Finished optimizer [2019-01-24 12:03:42.242] [jointLog] [info] writing output [2019-01-24 12:03:42.331] [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: bleached_K5_04/lib_format_counts.json for details [2019-01-24 12:42:52.116] [jointLog] [info] parsing read library format [2019-01-24 12:42:52.117] [jointLog] [info] There is 1 library. [2019-01-24 12:42:52.179] [jointLog] [info] Loading Quasi index [2019-01-24 12:42:52.179] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:42:54.905] [jointLog] [info] done [2019-01-24 12:42:54.905] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:44:01.678] [fileLog] [info] At end of round 0 ================== Observed 28323045 total fragments (28323045 in most recent round) [2019-01-24 12:44:01.677] [jointLog] [info] Computed 65041 rich equivalence classes for further processing [2019-01-24 12:44:01.677] [jointLog] [info] Counted 15162807 total reads in the equivalence classes [2019-01-24 12:44:01.686] [jointLog] [warning] 0.0118102% 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 12:44:01.686] [jointLog] [info] Mapping rate = 53.5352% [2019-01-24 12:44:01.686] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:44:01.686] [jointLog] [info] Starting optimizer [2019-01-24 12:44:01.719] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:44:01.721] [jointLog] [info] iteration = 0 | max rel diff. = 224.248 [2019-01-24 12:44:01.849] [jointLog] [info] iteration = 100 | max rel diff. = 0.113527 [2019-01-24 12:44:01.975] [jointLog] [info] iteration = 200 | max rel diff. = 0.0566742 [2019-01-24 12:44:02.098] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433018 [2019-01-24 12:44:02.223] [jointLog] [info] iteration = 400 | max rel diff. = 0.0278806 [2019-01-24 12:44:02.347] [jointLog] [info] iteration = 500 | max rel diff. = 0.0228845 [2019-01-24 12:44:02.472] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192233 [2019-01-24 12:44:02.601] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157824 [2019-01-24 12:44:02.727] [jointLog] [info] iteration = 800 | max rel diff. = 0.0150288 [2019-01-24 12:44:02.852] [jointLog] [info] iteration = 900 | max rel diff. = 0.0122231 [2019-01-24 12:44:02.978] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0122232 [2019-01-24 12:44:03.104] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0120087 [2019-01-24 12:44:03.232] [jointLog] [info] iteration = 1200 | max rel diff. = 0.010191 [2019-01-24 12:44:03.311] [jointLog] [info] iteration = 1263 | max rel diff. = 0.00892026 [2019-01-24 12:44:03.316] [jointLog] [info] Finished optimizer [2019-01-24 12:44:03.316] [jointLog] [info] writing output [2019-01-24 12:44:03.403] [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: bleached_K5_04/lib_format_counts.json for details [2019-01-24 20:31:59.405] [jointLog] [info] parsing read library format [2019-01-24 20:31:59.405] [jointLog] [info] There is 1 library. [2019-01-24 20:31:59.466] [jointLog] [info] Loading Quasi index [2019-01-24 20:31:59.466] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:32:02.323] [jointLog] [info] done [2019-01-24 20:32:02.323] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:33:09.509] [jointLog] [info] Computed 65041 rich equivalence classes for further processing [2019-01-24 20:33:09.509] [jointLog] [info] Counted 15162807 total reads in the equivalence classes [2019-01-24 20:33:09.517] [jointLog] [warning] 0.0118102% 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 20:33:09.517] [jointLog] [info] Mapping rate = 53.5352% [2019-01-24 20:33:09.517] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:33:09.517] [jointLog] [info] Starting optimizer [2019-01-24 20:33:09.546] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:33:09.547] [jointLog] [info] iteration = 0 | max rel diff. = 223.914 [2019-01-24 20:33:09.509] [fileLog] [info] At end of round 0 ================== Observed 28323045 total fragments (28323045 in most recent round) [2019-01-24 20:33:09.671] [jointLog] [info] iteration = 100 | max rel diff. = 0.113163 [2019-01-24 20:33:09.795] [jointLog] [info] iteration = 200 | max rel diff. = 0.0566745 [2019-01-24 20:33:09.919] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433007 [2019-01-24 20:33:10.044] [jointLog] [info] iteration = 400 | max rel diff. = 0.027911 [2019-01-24 20:33:10.169] [jointLog] [info] iteration = 500 | max rel diff. = 0.0229168 [2019-01-24 20:33:10.295] [jointLog] [info] iteration = 600 | max rel diff. = 0.019034 [2019-01-24 20:33:10.420] [jointLog] [info] iteration = 700 | max rel diff. = 0.0153454 [2019-01-24 20:33:10.549] [jointLog] [info] iteration = 800 | max rel diff. = 0.0149216 [2019-01-24 20:33:10.675] [jointLog] [info] iteration = 900 | max rel diff. = 0.0122229 [2019-01-24 20:33:10.802] [jointLog] [info] iteration = 1000 | max rel diff. = 0.012223 [2019-01-24 20:33:10.929] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0120077 [2019-01-24 20:33:11.057] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101907 [2019-01-24 20:33:11.136] [jointLog] [info] iteration = 1263 | max rel diff. = 0.0089341 [2019-01-24 20:33:11.141] [jointLog] [info] Finished optimizer [2019-01-24 20:33:11.141] [jointLog] [info] writing output [2019-01-24 20:33:11.228] [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: bleached_K5_04/lib_format_counts.json for details