[2019-01-24 12:01:20.600] [jointLog] [info] parsing read library format [2019-01-24 12:01:20.600] [jointLog] [info] There is 1 library. [2019-01-24 12:01:20.661] [jointLog] [info] Loading Quasi index [2019-01-24 12:01:20.661] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:01:23.734] [jointLog] [info] done [2019-01-24 12:01:23.734] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:02:25.233] [fileLog] [info] At end of round 0 ================== Observed 25906632 total fragments (25906632 in most recent round) [2019-01-24 12:02:25.233] [jointLog] [info] Computed 65922 rich equivalence classes for further processing [2019-01-24 12:02:25.233] [jointLog] [info] Counted 14021232 total reads in the equivalence classes [2019-01-24 12:02:25.242] [jointLog] [warning] 0.0136297% 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 12:02:25.242] [jointLog] [info] Mapping rate = 54.1222% [2019-01-24 12:02:25.242] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:02:25.242] [jointLog] [info] Starting optimizer [2019-01-24 12:02:25.278] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:02:25.279] [jointLog] [info] iteration = 0 | max rel diff. = 213.834 [2019-01-24 12:02:25.409] [jointLog] [info] iteration = 100 | max rel diff. = 0.121104 [2019-01-24 12:02:25.536] [jointLog] [info] iteration = 200 | max rel diff. = 0.0551123 [2019-01-24 12:02:25.665] [jointLog] [info] iteration = 300 | max rel diff. = 0.0397479 [2019-01-24 12:02:25.793] [jointLog] [info] iteration = 400 | max rel diff. = 0.0284187 [2019-01-24 12:02:25.922] [jointLog] [info] iteration = 500 | max rel diff. = 0.0221417 [2019-01-24 12:02:26.050] [jointLog] [info] iteration = 600 | max rel diff. = 0.0186584 [2019-01-24 12:02:26.178] [jointLog] [info] iteration = 700 | max rel diff. = 0.0178947 [2019-01-24 12:02:26.306] [jointLog] [info] iteration = 800 | max rel diff. = 0.013586 [2019-01-24 12:02:26.435] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126796 [2019-01-24 12:02:26.566] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0126797 [2019-01-24 12:02:26.696] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102734 [2019-01-24 12:02:26.827] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101704 [2019-01-24 12:02:26.852] [jointLog] [info] iteration = 1220 | max rel diff. = 0.00933251 [2019-01-24 12:02:26.857] [jointLog] [info] Finished optimizer [2019-01-24 12:02:26.857] [jointLog] [info] writing output [2019-01-24 12:02:26.944] [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_03/lib_format_counts.json for details [2019-01-24 12:41:47.220] [jointLog] [info] parsing read library format [2019-01-24 12:41:47.220] [jointLog] [info] There is 1 library. [2019-01-24 12:41:47.282] [jointLog] [info] Loading Quasi index [2019-01-24 12:41:47.282] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:41:50.146] [jointLog] [info] done [2019-01-24 12:41:50.146] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:42:48.956] [fileLog] [info] At end of round 0 ================== Observed 25906632 total fragments (25906632 in most recent round) [2019-01-24 12:42:48.955] [jointLog] [info] Computed 65922 rich equivalence classes for further processing [2019-01-24 12:42:48.955] [jointLog] [info] Counted 14021232 total reads in the equivalence classes [2019-01-24 12:42:48.964] [jointLog] [warning] 0.0136297% 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 12:42:48.964] [jointLog] [info] Mapping rate = 54.1222% [2019-01-24 12:42:48.964] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:42:48.964] [jointLog] [info] Starting optimizer [2019-01-24 12:42:49.000] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:42:49.001] [jointLog] [info] iteration = 0 | max rel diff. = 214.446 [2019-01-24 12:42:49.129] [jointLog] [info] iteration = 100 | max rel diff. = 0.121108 [2019-01-24 12:42:49.255] [jointLog] [info] iteration = 200 | max rel diff. = 0.0551149 [2019-01-24 12:42:49.381] [jointLog] [info] iteration = 300 | max rel diff. = 0.0397502 [2019-01-24 12:42:49.512] [jointLog] [info] iteration = 400 | max rel diff. = 0.0276394 [2019-01-24 12:42:49.640] [jointLog] [info] iteration = 500 | max rel diff. = 0.0222859 [2019-01-24 12:42:49.770] [jointLog] [info] iteration = 600 | max rel diff. = 0.0186605 [2019-01-24 12:42:49.900] [jointLog] [info] iteration = 700 | max rel diff. = 0.0176792 [2019-01-24 12:42:50.030] [jointLog] [info] iteration = 800 | max rel diff. = 0.0135864 [2019-01-24 12:42:50.160] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126804 [2019-01-24 12:42:50.287] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0126804 [2019-01-24 12:42:50.416] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102739 [2019-01-24 12:42:50.543] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101708 [2019-01-24 12:42:50.567] [jointLog] [info] iteration = 1220 | max rel diff. = 0.00939755 [2019-01-24 12:42:50.574] [jointLog] [info] Finished optimizer [2019-01-24 12:42:50.574] [jointLog] [info] writing output [2019-01-24 12:42:50.662] [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_03/lib_format_counts.json for details [2019-01-24 20:30:53.938] [jointLog] [info] parsing read library format [2019-01-24 20:30:53.938] [jointLog] [info] There is 1 library. [2019-01-24 20:30:54.000] [jointLog] [info] Loading Quasi index [2019-01-24 20:30:54.000] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:30:56.690] [jointLog] [info] done [2019-01-24 20:30:56.690] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:31:56.386] [jointLog] [info] Computed 65922 rich equivalence classes for further processing [2019-01-24 20:31:56.386] [jointLog] [info] Counted 14021232 total reads in the equivalence classes [2019-01-24 20:31:56.395] [jointLog] [warning] 0.0136297% 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 20:31:56.396] [jointLog] [info] Mapping rate = 54.1222% [2019-01-24 20:31:56.396] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:31:56.396] [jointLog] [info] Starting optimizer [2019-01-24 20:31:56.438] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:31:56.439] [jointLog] [info] iteration = 0 | max rel diff. = 213.842 [2019-01-24 20:31:56.569] [jointLog] [info] iteration = 100 | max rel diff. = 0.121097 [2019-01-24 20:31:56.387] [fileLog] [info] At end of round 0 ================== Observed 25906632 total fragments (25906632 in most recent round) [2019-01-24 20:31:56.694] [jointLog] [info] iteration = 200 | max rel diff. = 0.0551089 [2019-01-24 20:31:56.819] [jointLog] [info] iteration = 300 | max rel diff. = 0.0397445 [2019-01-24 20:31:56.947] [jointLog] [info] iteration = 400 | max rel diff. = 0.0284014 [2019-01-24 20:31:57.074] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243248 [2019-01-24 20:31:57.202] [jointLog] [info] iteration = 600 | max rel diff. = 0.0191207 [2019-01-24 20:31:57.329] [jointLog] [info] iteration = 700 | max rel diff. = 0.0180264 [2019-01-24 20:31:57.455] [jointLog] [info] iteration = 800 | max rel diff. = 0.0135852 [2019-01-24 20:31:57.582] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126782 [2019-01-24 20:31:57.709] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0126783 [2019-01-24 20:31:57.837] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107923 [2019-01-24 20:31:57.966] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101697 [2019-01-24 20:31:57.990] [jointLog] [info] iteration = 1220 | max rel diff. = 0.00874193 [2019-01-24 20:31:57.995] [jointLog] [info] Finished optimizer [2019-01-24 20:31:57.995] [jointLog] [info] writing output [2019-01-24 20:31:58.083] [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_03/lib_format_counts.json for details