[2023-08-26 00:22:40.588] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-26 00:22:40.588] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-26 00:22:40.588] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-26 00:22:40.588] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-26 00:22:40.588] [jointLog] [info] parsing read library format
[2023-08-26 00:22:40.588] [jointLog] [info] There is 1 library.
[2023-08-26 00:22:40.588] [jointLog] [info] Loading pufferfish index
[2023-08-26 00:22:40.588] [jointLog] [info] Loading dense pufferfish index.
[2023-08-26 00:24:01.981] [jointLog] [info] done
[2023-08-26 00:24:02.106] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-26 00:24:37.085] [jointLog] [info] Number of decoys : 194
[2023-08-26 00:24:37.085] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-26 00:24:40.010] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-26 00:31:50.959] [jointLog] [info] Thread saw mini-batch with a maximum of 6.62% zero probability fragments
[2023-08-26 00:31:50.976] [jointLog] [info] Thread saw mini-batch with a maximum of 6.44% zero probability fragments
[2023-08-26 00:31:51.074] [jointLog] [info] Thread saw mini-batch with a maximum of 6.78% zero probability fragments
[2023-08-26 00:31:51.113] [jointLog] [info] Thread saw mini-batch with a maximum of 6.42% zero probability fragments
[2023-08-26 00:31:51.195] [jointLog] [info] Thread saw mini-batch with a maximum of 6.48% zero probability fragments
[2023-08-26 00:31:51.230] [jointLog] [info] Thread saw mini-batch with a maximum of 6.44% zero probability fragments
[2023-08-26 00:31:51.274] [jointLog] [info] Thread saw mini-batch with a maximum of 6.60% zero probability fragments
[2023-08-26 00:31:51.341] [jointLog] [info] Thread saw mini-batch with a maximum of 6.50% zero probability fragments
[2023-08-26 00:31:51.909] [jointLog] [info] Computed 352,121 rich equivalence classes for further processing
[2023-08-26 00:31:51.909] [jointLog] [info] Counted 25,342,589 total reads in the equivalence classes 
[2023-08-26 00:31:51.919] [jointLog] [info] Number of mappings discarded because of alignment score : 19,805,063
[2023-08-26 00:31:51.919] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,542,817
[2023-08-26 00:31:51.919] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 2,468,979
[2023-08-26 00:31:51.919] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,677,022
[2023-08-26 00:31:51.919] [jointLog] [info] Mapping rate = 81.4003%

[2023-08-26 00:31:51.919] [jointLog] [info] finished quantifyLibrary()
[2023-08-26 00:31:51.920] [jointLog] [info] Starting optimizer
[2023-08-26 00:31:51.909] [fileLog] [info] 
At end of round 0
==================
Observed 31133279 total fragments (31133279 in most recent round)

[2023-08-26 00:31:57.540] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-26 00:31:57.897] [jointLog] [info] iteration = 0 | max rel diff. = 456.894
[2023-08-26 00:32:01.503] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-26 00:36:07.633] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-26 00:36:07.633] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-26 00:36:27.546] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-26 00:36:47.645] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-26 00:37:08.645] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-26 00:37:29.223] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-26 00:37:49.841] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-26 00:38:09.502] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-26 00:38:29.857] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-26 00:38:50.636] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-26 00:39:10.929] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-26 00:39:30.082] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-26 00:40:03.860] [jointLog] [info] iteration = 100 | max rel diff. = 14.4838
[2023-08-26 00:40:41.970] [jointLog] [info] iteration = 200 | max rel diff. = 16.4203
[2023-08-26 00:41:19.591] [jointLog] [info] iteration = 300 | max rel diff. = 2.51598
[2023-08-26 00:41:55.915] [jointLog] [info] iteration = 400 | max rel diff. = 3.08031
[2023-08-26 00:42:31.588] [jointLog] [info] iteration = 500 | max rel diff. = 0.168431
[2023-08-26 00:43:07.823] [jointLog] [info] iteration = 600 | max rel diff. = 0.0738455
[2023-08-26 00:43:43.954] [jointLog] [info] iteration = 700 | max rel diff. = 0.6984
[2023-08-26 00:44:20.295] [jointLog] [info] iteration = 800 | max rel diff. = 0.0403397
[2023-08-26 00:44:56.639] [jointLog] [info] iteration = 900 | max rel diff. = 0.17796
[2023-08-26 00:45:32.962] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.19158
[2023-08-26 00:46:09.123] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0294831
[2023-08-26 00:46:45.173] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.255703
[2023-08-26 00:47:21.475] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.079021
[2023-08-26 00:47:45.333] [jointLog] [info] iteration = 1,367 | max rel diff. = 0.00618856
[2023-08-26 00:47:47.907] [jointLog] [info] Finished optimizer
[2023-08-26 00:47:47.907] [jointLog] [info] writing output