[2019-01-24 12:05:24.047] [jointLog] [info] parsing read library format [2019-01-24 12:05:24.047] [jointLog] [info] There is 1 library. [2019-01-24 12:05:24.107] [jointLog] [info] Loading Quasi index [2019-01-24 12:05:24.107] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:05:26.922] [jointLog] [info] done [2019-01-24 12:05:26.922] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:06:23.942] [jointLog] [info] Computed 69834 rich equivalence classes for further processing [2019-01-24 12:06:23.942] [jointLog] [info] Counted 10972275 total reads in the equivalence classes [2019-01-24 12:06:23.951] [jointLog] [warning] 0.0188665% 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 12:06:23.951] [jointLog] [info] Mapping rate = 47.6538% [2019-01-24 12:06:23.951] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:06:23.951] [jointLog] [info] Starting optimizer [2019-01-24 12:06:24.005] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:06:24.007] [jointLog] [info] iteration = 0 | max rel diff. = 194.897 [2019-01-24 12:06:23.943] [fileLog] [info] At end of round 0 ================== Observed 23024986 total fragments (23024986 in most recent round) [2019-01-24 12:06:24.135] [jointLog] [info] iteration = 100 | max rel diff. = 0.10839 [2019-01-24 12:06:24.261] [jointLog] [info] iteration = 200 | max rel diff. = 0.055573 [2019-01-24 12:06:24.387] [jointLog] [info] iteration = 300 | max rel diff. = 0.041701 [2019-01-24 12:06:24.517] [jointLog] [info] iteration = 400 | max rel diff. = 0.02685 [2019-01-24 12:06:24.643] [jointLog] [info] iteration = 500 | max rel diff. = 0.0226664 [2019-01-24 12:06:24.770] [jointLog] [info] iteration = 600 | max rel diff. = 0.020127 [2019-01-24 12:06:24.899] [jointLog] [info] iteration = 700 | max rel diff. = 0.0162506 [2019-01-24 12:06:25.026] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142882 [2019-01-24 12:06:25.153] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142882 [2019-01-24 12:06:25.281] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0111969 [2019-01-24 12:06:25.409] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0111382 [2019-01-24 12:06:25.504] [jointLog] [info] iteration = 1175 | max rel diff. = 0.00973005 [2019-01-24 12:06:25.509] [jointLog] [info] Finished optimizer [2019-01-24 12:06:25.509] [jointLog] [info] writing output [2019-01-24 12:06:25.598] [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_44_01/lib_format_counts.json for details [2019-01-24 12:45:42.480] [jointLog] [info] parsing read library format [2019-01-24 12:45:42.480] [jointLog] [info] There is 1 library. [2019-01-24 12:45:42.542] [jointLog] [info] Loading Quasi index [2019-01-24 12:45:42.542] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 12:45:45.410] [jointLog] [info] done [2019-01-24 12:45:45.410] [jointLog] [info] Index contained 49695 targets [2019-01-24 12:46:40.139] [jointLog] [info] Computed 69834 rich equivalence classes for further processing [2019-01-24 12:46:40.139] [jointLog] [info] Counted 10972275 total reads in the equivalence classes [2019-01-24 12:46:40.148] [jointLog] [warning] 0.0188665% 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 12:46:40.148] [jointLog] [info] Mapping rate = 47.6538% [2019-01-24 12:46:40.148] [jointLog] [info] finished quantifyLibrary() [2019-01-24 12:46:40.148] [jointLog] [info] Starting optimizer [2019-01-24 12:46:40.183] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 12:46:40.184] [jointLog] [info] iteration = 0 | max rel diff. = 195.159 [2019-01-24 12:46:40.140] [fileLog] [info] At end of round 0 ================== Observed 23024986 total fragments (23024986 in most recent round) [2019-01-24 12:46:40.316] [jointLog] [info] iteration = 100 | max rel diff. = 0.108352 [2019-01-24 12:46:40.444] [jointLog] [info] iteration = 200 | max rel diff. = 0.055573 [2019-01-24 12:46:40.573] [jointLog] [info] iteration = 300 | max rel diff. = 0.041759 [2019-01-24 12:46:40.702] [jointLog] [info] iteration = 400 | max rel diff. = 0.0292488 [2019-01-24 12:46:40.833] [jointLog] [info] iteration = 500 | max rel diff. = 0.0226668 [2019-01-24 12:46:40.963] [jointLog] [info] iteration = 600 | max rel diff. = 0.0201127 [2019-01-24 12:46:41.093] [jointLog] [info] iteration = 700 | max rel diff. = 0.0162533 [2019-01-24 12:46:41.224] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142864 [2019-01-24 12:46:41.354] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142864 [2019-01-24 12:46:41.489] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0111977 [2019-01-24 12:46:41.623] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0108862 [2019-01-24 12:46:41.654] [jointLog] [info] iteration = 1125 | max rel diff. = 0.00972029 [2019-01-24 12:46:41.659] [jointLog] [info] Finished optimizer [2019-01-24 12:46:41.659] [jointLog] [info] writing output [2019-01-24 12:46:41.758] [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_44_01/lib_format_counts.json for details [2019-01-24 20:34:52.452] [jointLog] [info] parsing read library format [2019-01-24 20:34:52.452] [jointLog] [info] There is 1 library. [2019-01-24 20:34:52.511] [jointLog] [info] Loading Quasi index [2019-01-24 20:34:52.512] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:34:55.358] [jointLog] [info] done [2019-01-24 20:34:55.358] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:35:49.734] [jointLog] [info] Computed 69834 rich equivalence classes for further processing [2019-01-24 20:35:49.734] [jointLog] [info] Counted 10972275 total reads in the equivalence classes [2019-01-24 20:35:49.742] [jointLog] [warning] 0.0188665% 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 20:35:49.742] [jointLog] [info] Mapping rate = 47.6538% [2019-01-24 20:35:49.742] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:35:49.742] [jointLog] [info] Starting optimizer [2019-01-24 20:35:49.779] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:35:49.781] [jointLog] [info] iteration = 0 | max rel diff. = 194.902 [2019-01-24 20:35:49.734] [fileLog] [info] At end of round 0 ================== Observed 23024986 total fragments (23024986 in most recent round) [2019-01-24 20:35:49.909] [jointLog] [info] iteration = 100 | max rel diff. = 0.10837 [2019-01-24 20:35:50.038] [jointLog] [info] iteration = 200 | max rel diff. = 0.055573 [2019-01-24 20:35:50.168] [jointLog] [info] iteration = 300 | max rel diff. = 0.041752 [2019-01-24 20:35:50.298] [jointLog] [info] iteration = 400 | max rel diff. = 0.0294721 [2019-01-24 20:35:50.427] [jointLog] [info] iteration = 500 | max rel diff. = 0.0244157 [2019-01-24 20:35:50.557] [jointLog] [info] iteration = 600 | max rel diff. = 0.0187225 [2019-01-24 20:35:50.692] [jointLog] [info] iteration = 700 | max rel diff. = 0.0162498 [2019-01-24 20:35:50.824] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142847 [2019-01-24 20:35:50.955] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142847 [2019-01-24 20:35:51.087] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116814 [2019-01-24 20:35:51.218] [jointLog] [info] iteration = 1100 | max rel diff. = 0.00973188 [2019-01-24 20:35:51.222] [jointLog] [info] Finished optimizer [2019-01-24 20:35:51.222] [jointLog] [info] writing output [2019-01-24 20:35:51.317] [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_44_01/lib_format_counts.json for details