[2022-12-20 23:56:18.708] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:56:18.708] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:56:18.708] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:56:18.708] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:56:18.708] [jointLog] [info] parsing read library format
[2022-12-20 23:56:18.708] [jointLog] [info] There is 1 library.
[2022-12-20 23:56:18.708] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:56:18.708] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:56:36.984] [jointLog] [info] done
[2022-12-20 23:56:37.046] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:56:37.534] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:56:37.534] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:56:38.361] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-21 00:00:42.946] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:00:42.951] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-21 00:00:42.959] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-21 00:00:42.991] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments
[2022-12-21 00:00:43.011] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-21 00:00:43.017] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-21 00:00:43.071] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-21 00:00:43.236] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-21 00:00:43.461] [jointLog] [info] Computed 264,165 rich equivalence classes for further processing
[2022-12-21 00:00:43.461] [jointLog] [info] Counted 13,261,494 total reads in the equivalence classes 
[2022-12-21 00:00:43.466] [jointLog] [info] Number of mappings discarded because of alignment score : 53,320,450
[2022-12-21 00:00:43.466] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,817,609
[2022-12-21 00:00:43.466] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 287,890
[2022-12-21 00:00:43.466] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 7,931,464
[2022-12-21 00:00:43.466] [jointLog] [info] Mapping rate = 66.2399%

[2022-12-21 00:00:43.466] [jointLog] [info] finished quantifyLibrary()
[2022-12-21 00:00:43.490] [jointLog] [info] Starting optimizer
[2022-12-21 00:00:43.577] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-21 00:00:43.591] [jointLog] [info] iteration = 0 | max rel diff. = 6529.18
[2022-12-21 00:00:43.716] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-21 00:00:43.461] [fileLog] [info] 
At end of round 0
==================
Observed 20020409 total fragments (20020409 in most recent round)

[2022-12-21 00:00:44.686] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-21 00:00:44.686] [jointLog] [info] processed bias for 0.1% of the transcripts
[2022-12-21 00:00:45.250] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-21 00:00:45.846] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-21 00:00:46.481] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-21 00:00:47.057] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-21 00:00:47.522] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-21 00:00:47.990] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-21 00:00:48.466] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-21 00:00:48.946] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-21 00:00:49.396] [jointLog] [info] processed bias for 90.1% of the transcripts
[2022-12-21 00:00:50.020] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-21 00:00:50.021] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-21 00:00:51.440] [jointLog] [info] iteration = 100 | max rel diff. = 18.8932
[2022-12-21 00:00:53.471] [jointLog] [info] iteration = 200 | max rel diff. = 6.32083
[2022-12-21 00:00:55.111] [jointLog] [info] iteration = 300 | max rel diff. = 1.97251
[2022-12-21 00:00:56.374] [jointLog] [info] iteration = 400 | max rel diff. = 0.233721
[2022-12-21 00:00:57.634] [jointLog] [info] iteration = 500 | max rel diff. = 0.329656
[2022-12-21 00:00:58.878] [jointLog] [info] iteration = 600 | max rel diff. = 0.082476
[2022-12-21 00:01:00.047] [jointLog] [info] iteration = 700 | max rel diff. = 0.24916
[2022-12-21 00:01:01.226] [jointLog] [info] iteration = 800 | max rel diff. = 0.0531251
[2022-12-21 00:01:02.572] [jointLog] [info] iteration = 900 | max rel diff. = 2.75482
[2022-12-21 00:01:03.798] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0380769
[2022-12-21 00:01:05.058] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0181406
[2022-12-21 00:01:06.208] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.132761
[2022-12-21 00:01:06.619] [jointLog] [info] iteration = 1,236 | max rel diff. = 0.00733005
[2022-12-21 00:01:06.639] [jointLog] [info] Finished optimizer
[2022-12-21 00:01:06.639] [jointLog] [info] writing output