[2022-12-20 23:46:48.020] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:46:48.020] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:46:48.020] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:46:48.020] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:46:48.020] [jointLog] [info] parsing read library format
[2022-12-20 23:46:48.020] [jointLog] [info] There is 1 library.
[2022-12-20 23:46:48.020] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:46:48.020] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:47:14.791] [jointLog] [info] done
[2022-12-20 23:47:14.842] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:47:15.332] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:47:15.332] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:47:16.164] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-20 23:51:47.448] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:51:47.467] [jointLog] [info] Thread saw mini-batch with a maximum of 0.32% zero probability fragments
[2022-12-20 23:51:47.507] [jointLog] [info] Thread saw mini-batch with a maximum of 0.32% zero probability fragments
[2022-12-20 23:51:47.521] [jointLog] [info] Thread saw mini-batch with a maximum of 0.34% zero probability fragments
[2022-12-20 23:51:47.526] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:51:47.638] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:51:47.658] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:51:47.690] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:51:47.878] [jointLog] [info] Computed 273,759 rich equivalence classes for further processing
[2022-12-20 23:51:47.878] [jointLog] [info] Counted 15,377,334 total reads in the equivalence classes 
[2022-12-20 23:51:47.883] [jointLog] [info] Number of mappings discarded because of alignment score : 33,823,448
[2022-12-20 23:51:47.883] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,462,648
[2022-12-20 23:51:47.883] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 317,059
[2022-12-20 23:51:47.883] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,507,092
[2022-12-20 23:51:47.883] [jointLog] [info] Mapping rate = 77.1183%

[2022-12-20 23:51:47.883] [jointLog] [info] finished quantifyLibrary()
[2022-12-20 23:51:47.883] [jointLog] [info] Starting optimizer
[2022-12-20 23:51:47.953] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-20 23:51:47.968] [jointLog] [info] iteration = 0 | max rel diff. = 7151.73
[2022-12-20 23:51:48.098] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-20 23:51:47.878] [fileLog] [info] 
At end of round 0
==================
Observed 19939929 total fragments (19939929 in most recent round)

[2022-12-20 23:51:48.942] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-20 23:51:48.943] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-12-20 23:51:49.454] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-20 23:51:50.009] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-20 23:51:50.549] [jointLog] [info] processed bias for 30.1% of the transcripts
[2022-12-20 23:51:51.083] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-20 23:51:51.626] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-20 23:51:52.173] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-20 23:51:52.684] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-20 23:51:53.178] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-20 23:51:53.765] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-20 23:51:54.246] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:51:54.248] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:51:55.312] [jointLog] [info] iteration = 100 | max rel diff. = 14.2018
[2022-12-20 23:51:56.511] [jointLog] [info] iteration = 200 | max rel diff. = 13.1062
[2022-12-20 23:51:57.718] [jointLog] [info] iteration = 300 | max rel diff. = 1.46189
[2022-12-20 23:51:58.928] [jointLog] [info] iteration = 400 | max rel diff. = 0.368287
[2022-12-20 23:52:00.126] [jointLog] [info] iteration = 500 | max rel diff. = 0.310047
[2022-12-20 23:52:01.330] [jointLog] [info] iteration = 600 | max rel diff. = 2.52391
[2022-12-20 23:52:02.536] [jointLog] [info] iteration = 700 | max rel diff. = 3.65762
[2022-12-20 23:52:03.734] [jointLog] [info] iteration = 800 | max rel diff. = 0.10602
[2022-12-20 23:52:04.948] [jointLog] [info] iteration = 900 | max rel diff. = 0.136902
[2022-12-20 23:52:06.155] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.040496
[2022-12-20 23:52:07.352] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0751066
[2022-12-20 23:52:08.556] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.163902
[2022-12-20 23:52:09.764] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0534531
[2022-12-20 23:52:11.127] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.00748159
[2022-12-20 23:52:11.146] [jointLog] [info] Finished optimizer
[2022-12-20 23:52:11.146] [jointLog] [info] writing output