[2023-08-28 15:16:16.273] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 15:16:16.273] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 15:16:16.273] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 15:16:16.273] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 15:16:16.273] [jointLog] [info] parsing read library format
[2023-08-28 15:16:16.274] [jointLog] [info] There is 1 library.
[2023-08-28 15:16:16.274] [jointLog] [info] Loading pufferfish index
[2023-08-28 15:16:16.274] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 15:17:43.683] [jointLog] [info] done
[2023-08-28 15:17:43.842] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 15:18:24.035] [jointLog] [info] Number of decoys : 194
[2023-08-28 15:18:24.035] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 15:18:29.363] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-28 15:26:02.620] [jointLog] [info] Thread saw mini-batch with a maximum of 19.52% zero probability fragments
[2023-08-28 15:26:02.815] [jointLog] [info] Thread saw mini-batch with a maximum of 19.58% zero probability fragments
[2023-08-28 15:26:02.928] [jointLog] [info] Thread saw mini-batch with a maximum of 19.62% zero probability fragments
[2023-08-28 15:26:02.992] [jointLog] [info] Thread saw mini-batch with a maximum of 20.14% zero probability fragments
[2023-08-28 15:26:03.027] [jointLog] [info] Thread saw mini-batch with a maximum of 19.66% zero probability fragments
[2023-08-28 15:26:03.145] [jointLog] [info] Thread saw mini-batch with a maximum of 19.72% zero probability fragments
[2023-08-28 15:26:03.774] [jointLog] [info] Thread saw mini-batch with a maximum of 19.54% zero probability fragments
[2023-08-28 15:26:03.884] [jointLog] [info] Thread saw mini-batch with a maximum of 19.60% zero probability fragments
[2023-08-28 15:26:04.403] [fileLog] [info] 
At end of round 0
==================
Observed 11714778 total fragments (11714778 in most recent round)

[2023-08-28 15:26:04.402] [jointLog] [info] Computed 357,324 rich equivalence classes for further processing
[2023-08-28 15:26:04.402] [jointLog] [info] Counted 7,354,557 total reads in the equivalence classes 
[2023-08-28 15:26:04.409] [jointLog] [info] Number of mappings discarded because of alignment score : 44,548,057
[2023-08-28 15:26:04.409] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,094,926
[2023-08-28 15:26:04.409] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 504,742
[2023-08-28 15:26:04.409] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,951,916
[2023-08-28 15:26:04.409] [jointLog] [info] Mapping rate = 62.7802%

[2023-08-28 15:26:04.409] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 15:26:04.410] [jointLog] [info] Starting optimizer
[2023-08-28 15:26:08.800] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 15:26:09.151] [jointLog] [info] iteration = 0 | max rel diff. = 153.573
[2023-08-28 15:26:12.720] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 15:28:49.118] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 15:28:49.118] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 15:29:03.976] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 15:29:18.863] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 15:29:33.558] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 15:29:47.587] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 15:30:02.437] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 15:30:18.335] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 15:30:33.911] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 15:30:48.524] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 15:31:03.349] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 15:31:20.632] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 15:31:53.443] [jointLog] [info] iteration = 100 | max rel diff. = 16.894
[2023-08-28 15:32:29.108] [jointLog] [info] iteration = 200 | max rel diff. = 11.2199
[2023-08-28 15:33:04.425] [jointLog] [info] iteration = 300 | max rel diff. = 1.41844
[2023-08-28 15:33:40.328] [jointLog] [info] iteration = 400 | max rel diff. = 2.70548
[2023-08-28 15:34:15.139] [jointLog] [info] iteration = 500 | max rel diff. = 2.33589
[2023-08-28 15:34:50.271] [jointLog] [info] iteration = 600 | max rel diff. = 0.125836
[2023-08-28 15:35:25.653] [jointLog] [info] iteration = 700 | max rel diff. = 0.0312502
[2023-08-28 15:36:01.464] [jointLog] [info] iteration = 800 | max rel diff. = 2.82465
[2023-08-28 15:36:36.384] [jointLog] [info] iteration = 900 | max rel diff. = 0.864586
[2023-08-28 15:37:05.401] [jointLog] [info] iteration = 985 | max rel diff. = 0.00255515
[2023-08-28 15:37:07.402] [jointLog] [info] Finished optimizer
[2023-08-28 15:37:07.402] [jointLog] [info] writing output