[2022-12-20 23:51:48.525] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:51:48.525] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:51:48.525] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:51:48.525] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:51:48.525] [jointLog] [info] parsing read library format
[2022-12-20 23:51:48.525] [jointLog] [info] There is 1 library.
[2022-12-20 23:51:48.525] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:51:48.525] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:52:09.318] [jointLog] [info] done
[2022-12-20 23:52:09.361] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:52:09.657] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:52:09.657] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:52:10.319] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-20 23:55:46.876] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:55:46.896] [jointLog] [info] Thread saw mini-batch with a maximum of 0.32% zero probability fragments
[2022-12-20 23:55:46.900] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:55:46.927] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:55:46.944] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-20 23:55:46.983] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:55:47.036] [jointLog] [info] Thread saw mini-batch with a maximum of 0.32% zero probability fragments
[2022-12-20 23:55:47.098] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:55:47.367] [jointLog] [info] Computed 266,058 rich equivalence classes for further processing
[2022-12-20 23:55:47.367] [jointLog] [info] Counted 13,726,455 total reads in the equivalence classes 
[2022-12-20 23:55:47.372] [jointLog] [info] Number of mappings discarded because of alignment score : 37,706,952
[2022-12-20 23:55:47.372] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,058,469
[2022-12-20 23:55:47.372] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 294,335
[2022-12-20 23:55:47.372] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,282,086
[2022-12-20 23:55:47.372] [jointLog] [info] Mapping rate = 74.0144%

[2022-12-20 23:55:47.372] [jointLog] [info] finished quantifyLibrary()
[2022-12-20 23:55:47.510] [jointLog] [info] Starting optimizer
[2022-12-20 23:55:47.599] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-20 23:55:47.614] [jointLog] [info] iteration = 0 | max rel diff. = 6703.91
[2022-12-20 23:55:47.367] [fileLog] [info] 
At end of round 0
==================
Observed 18545652 total fragments (18545652 in most recent round)

[2022-12-20 23:55:47.756] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-20 23:55:49.079] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-20 23:55:49.080] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-12-20 23:55:49.936] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-20 23:55:50.910] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-20 23:55:51.826] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-20 23:55:52.485] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-20 23:55:53.063] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-20 23:55:53.591] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-20 23:55:54.083] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-20 23:55:54.625] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-20 23:55:55.191] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-20 23:55:55.737] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:55:55.739] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:55:56.777] [jointLog] [info] iteration = 100 | max rel diff. = 17.1722
[2022-12-20 23:55:57.983] [jointLog] [info] iteration = 200 | max rel diff. = 6.07929
[2022-12-20 23:55:59.142] [jointLog] [info] iteration = 300 | max rel diff. = 6.49243
[2022-12-20 23:56:00.319] [jointLog] [info] iteration = 400 | max rel diff. = 5.0218
[2022-12-20 23:56:01.454] [jointLog] [info] iteration = 500 | max rel diff. = 1.35616
[2022-12-20 23:56:02.585] [jointLog] [info] iteration = 600 | max rel diff. = 0.347468
[2022-12-20 23:56:03.746] [jointLog] [info] iteration = 700 | max rel diff. = 0.172838
[2022-12-20 23:56:04.921] [jointLog] [info] iteration = 800 | max rel diff. = 8.04745
[2022-12-20 23:56:06.067] [jointLog] [info] iteration = 900 | max rel diff. = 0.0518375
[2022-12-20 23:56:07.229] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0779345
[2022-12-20 23:56:08.415] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0661503
[2022-12-20 23:56:09.566] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.145602
[2022-12-20 23:56:10.740] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.270708
[2022-12-20 23:56:11.929] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0505421
[2022-12-20 23:56:13.122] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.27053
[2022-12-20 23:56:14.315] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0181914
[2022-12-20 23:56:15.437] [jointLog] [info] iteration = 1,695 | max rel diff. = 0.00481016
[2022-12-20 23:56:15.455] [jointLog] [info] Finished optimizer
[2022-12-20 23:56:15.455] [jointLog] [info] writing output