[2023-01-05 17:45:50.255] [jointLog] [info] setting maxHashResizeThreads to 24
[2023-01-05 17:45:50.255] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-01-05 17:45:50.255] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-01-05 17:45:50.255] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-01-05 17:45:50.255] [jointLog] [info] parsing read library format
[2023-01-05 17:45:50.255] [jointLog] [info] There is 1 library.
[2023-01-05 17:45:50.255] [jointLog] [info] Loading pufferfish index
[2023-01-05 17:45:50.255] [jointLog] [info] Loading dense pufferfish index.
[2023-01-05 17:46:55.391] [jointLog] [info] done
[2023-01-05 17:46:55.466] [jointLog] [info] Index contained 5,382,683 targets
[2023-01-05 17:47:30.344] [jointLog] [info] Number of decoys : 194
[2023-01-05 17:47:30.344] [jointLog] [info] First decoy index : 5,185,409 
[2023-01-05 17:47:33.182] [jointLog] [info] Automatically detected most likely library type as IU

[2023-01-05 17:49:01.621] [fileLog] [info] 
At end of round 0
==================
Observed 20120088 total fragments (20120088 in most recent round)

[2023-01-05 17:49:01.620] [jointLog] [info] Computed 237,475 rich equivalence classes for further processing
[2023-01-05 17:49:01.620] [jointLog] [info] Counted 18,806,691 total reads in the equivalence classes 
[2023-01-05 17:49:01.644] [jointLog] [info] Number of mappings discarded because of alignment score : 7,878,722
[2023-01-05 17:49:01.644] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,181,172
[2023-01-05 17:49:01.644] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 474,881
[2023-01-05 17:49:01.644] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 716,604
[2023-01-05 17:49:01.644] [jointLog] [info] Mapping rate = 93.4722%

[2023-01-05 17:49:01.644] [jointLog] [info] finished quantifyLibrary()
[2023-01-05 17:49:01.645] [jointLog] [info] Starting optimizer
[2023-01-05 17:49:13.097] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-01-05 17:49:13.381] [jointLog] [info] iteration = 0 | max rel diff. = 296.86
[2023-01-05 17:49:16.165] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-01-05 17:50:19.651] [jointLog] [info] Computed expected counts (for bias correction)
[2023-01-05 17:50:19.652] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-01-05 17:50:24.786] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-01-05 17:50:30.035] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-01-05 17:50:35.373] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-01-05 17:50:40.442] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-01-05 17:50:45.919] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-01-05 17:50:51.082] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-01-05 17:50:56.428] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-01-05 17:51:01.825] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-01-05 17:51:07.281] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-01-05 17:51:13.117] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-01-05 17:51:39.094] [jointLog] [info] iteration = 100 | max rel diff. = 13.7997
[2023-01-05 17:52:07.320] [jointLog] [info] iteration = 200 | max rel diff. = 6.29526
[2023-01-05 17:52:35.036] [jointLog] [info] iteration = 300 | max rel diff. = 3.45724
[2023-01-05 17:53:02.677] [jointLog] [info] iteration = 400 | max rel diff. = 14.1468
[2023-01-05 17:53:30.398] [jointLog] [info] iteration = 500 | max rel diff. = 0.329576
[2023-01-05 17:53:57.942] [jointLog] [info] iteration = 600 | max rel diff. = 0.216105
[2023-01-05 17:54:25.414] [jointLog] [info] iteration = 700 | max rel diff. = 0.0851087
[2023-01-05 17:54:52.874] [jointLog] [info] iteration = 800 | max rel diff. = 0.295161
[2023-01-05 17:54:55.878] [jointLog] [info] iteration = 812 | max rel diff. = 0.0067627
[2023-01-05 17:54:57.759] [jointLog] [info] Finished optimizer
[2023-01-05 17:54:57.759] [jointLog] [info] writing output