[2023-09-08 02:12:14.928] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-08 02:12:14.928] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-08 02:12:14.928] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-08 02:12:14.928] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-08 02:12:14.928] [jointLog] [info] parsing read library format
[2023-09-08 02:12:14.928] [jointLog] [info] There is 1 library.
[2023-09-08 02:12:14.928] [jointLog] [info] Loading pufferfish index
[2023-09-08 02:12:14.928] [jointLog] [info] Loading dense pufferfish index.
[2023-09-08 02:13:30.218] [jointLog] [info] done
[2023-09-08 02:13:30.348] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-08 02:14:05.657] [jointLog] [info] Number of decoys : 194
[2023-09-08 02:14:05.657] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-08 02:14:08.347] [jointLog] [info] Automatically detected most likely library type as IU

[2023-09-08 02:20:38.462] [fileLog] [info] 
At end of round 0
==================
Observed 25925949 total fragments (25925949 in most recent round)

[2023-09-08 02:20:38.461] [jointLog] [info] Computed 308,371 rich equivalence classes for further processing
[2023-09-08 02:20:38.461] [jointLog] [info] Counted 23,735,012 total reads in the equivalence classes 
[2023-09-08 02:20:38.472] [jointLog] [info] Number of mappings discarded because of alignment score : 10,592,161
[2023-09-08 02:20:38.472] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,013,745
[2023-09-08 02:20:38.472] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 688,582
[2023-09-08 02:20:38.472] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 388,543
[2023-09-08 02:20:38.472] [jointLog] [info] Mapping rate = 91.5493%

[2023-09-08 02:20:38.473] [jointLog] [info] finished quantifyLibrary()
[2023-09-08 02:20:38.474] [jointLog] [info] Starting optimizer
[2023-09-08 02:20:43.157] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-08 02:20:43.518] [jointLog] [info] iteration = 0 | max rel diff. = 250.996
[2023-09-08 02:20:47.084] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-08 02:25:20.562] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-08 02:25:20.563] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-08 02:25:43.018] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-08 02:26:05.153] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-08 02:26:27.574] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-08 02:26:49.979] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-08 02:27:12.785] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-08 02:27:35.938] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-08 02:27:58.041] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-08 02:28:20.679] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-08 02:28:43.258] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-08 02:29:05.599] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-08 02:29:05.607] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-08 02:29:38.509] [jointLog] [info] iteration = 100 | max rel diff. = 15.4214
[2023-09-08 02:30:14.898] [jointLog] [info] iteration = 200 | max rel diff. = 12.2276
[2023-09-08 02:30:51.339] [jointLog] [info] iteration = 300 | max rel diff. = 0.29444
[2023-09-08 02:31:27.727] [jointLog] [info] iteration = 400 | max rel diff. = 0.222256
[2023-09-08 02:32:04.047] [jointLog] [info] iteration = 500 | max rel diff. = 0.130607
[2023-09-08 02:32:40.467] [jointLog] [info] iteration = 600 | max rel diff. = 0.419407
[2023-09-08 02:33:16.774] [jointLog] [info] iteration = 700 | max rel diff. = 0.0267752
[2023-09-08 02:33:52.344] [jointLog] [info] iteration = 800 | max rel diff. = 0.157462
[2023-09-08 02:34:28.118] [jointLog] [info] iteration = 900 | max rel diff. = 0.0215383
[2023-09-08 02:35:03.872] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.117397
[2023-09-08 02:35:39.258] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.329975
[2023-09-08 02:36:14.900] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0281528
[2023-09-08 02:36:50.063] [jointLog] [info] iteration = 1,299 | max rel diff. = 0.0065355
[2023-09-08 02:36:52.275] [jointLog] [info] Finished optimizer
[2023-09-08 02:36:52.275] [jointLog] [info] writing output