[2023-09-01 22:26:14.399] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-01 22:26:14.399] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-01 22:26:14.399] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-01 22:26:14.399] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-01 22:26:14.399] [jointLog] [info] parsing read library format
[2023-09-01 22:26:14.399] [jointLog] [info] There is 1 library.
[2023-09-01 22:26:14.399] [jointLog] [info] Loading pufferfish index
[2023-09-01 22:26:14.399] [jointLog] [info] Loading dense pufferfish index.
[2023-09-01 22:27:33.606] [jointLog] [info] done
[2023-09-01 22:27:33.723] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-01 22:28:09.349] [jointLog] [info] Number of decoys : 194
[2023-09-01 22:28:09.349] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-01 22:28:11.879] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-01 22:42:50.210] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments
[2023-09-01 22:42:50.393] [jointLog] [info] Thread saw mini-batch with a maximum of 2.36% zero probability fragments
[2023-09-01 22:42:50.596] [jointLog] [info] Thread saw mini-batch with a maximum of 2.34% zero probability fragments
[2023-09-01 22:42:50.722] [jointLog] [info] Thread saw mini-batch with a maximum of 2.24% zero probability fragments
[2023-09-01 22:42:50.723] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments
[2023-09-01 22:42:50.753] [jointLog] [info] Thread saw mini-batch with a maximum of 2.32% zero probability fragments
[2023-09-01 22:42:50.801] [jointLog] [info] Thread saw mini-batch with a maximum of 2.24% zero probability fragments
[2023-09-01 22:42:50.908] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments
[2023-09-01 22:42:51.508] [jointLog] [info] Computed 421,433 rich equivalence classes for further processing
[2023-09-01 22:42:51.508] [jointLog] [info] Counted 57,865,113 total reads in the equivalence classes 
[2023-09-01 22:42:51.519] [jointLog] [info] Number of mappings discarded because of alignment score : 32,373,701
[2023-09-01 22:42:51.519] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,440,295
[2023-09-01 22:42:51.519] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,346,852
[2023-09-01 22:42:51.519] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 7,482,091
[2023-09-01 22:42:51.519] [jointLog] [info] Mapping rate = 92.0272%

[2023-09-01 22:42:51.519] [jointLog] [info] finished quantifyLibrary()
[2023-09-01 22:42:51.520] [jointLog] [info] Starting optimizer
[2023-09-01 22:42:51.509] [fileLog] [info] 
At end of round 0
==================
Observed 62878268 total fragments (62878268 in most recent round)

[2023-09-01 22:42:57.097] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-01 22:42:57.452] [jointLog] [info] iteration = 0 | max rel diff. = 143.208
[2023-09-01 22:43:01.011] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-01 22:45:39.734] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-01 22:45:39.735] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-01 22:45:52.675] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-01 22:46:06.188] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-01 22:46:20.049] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-01 22:46:33.945] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-01 22:46:47.508] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-01 22:47:01.017] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-01 22:47:14.640] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-01 22:47:27.616] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-01 22:47:41.199] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-01 22:47:54.811] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-01 22:48:26.731] [jointLog] [info] iteration = 100 | max rel diff. = 14.6113
[2023-09-01 22:49:01.771] [jointLog] [info] iteration = 200 | max rel diff. = 6.12152
[2023-09-01 22:49:37.188] [jointLog] [info] iteration = 300 | max rel diff. = 0.667629
[2023-09-01 22:50:12.033] [jointLog] [info] iteration = 400 | max rel diff. = 0.262644
[2023-09-01 22:50:46.266] [jointLog] [info] iteration = 500 | max rel diff. = 0.0738047
[2023-09-01 22:51:20.707] [jointLog] [info] iteration = 600 | max rel diff. = 0.0367
[2023-09-01 22:51:55.030] [jointLog] [info] iteration = 700 | max rel diff. = 0.587169
[2023-09-01 22:52:28.872] [jointLog] [info] iteration = 800 | max rel diff. = 0.820487
[2023-09-01 22:53:03.130] [jointLog] [info] iteration = 900 | max rel diff. = 0.116062
[2023-09-01 22:53:37.231] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.108792
[2023-09-01 22:54:06.193] [jointLog] [info] iteration = 1,086 | max rel diff. = 0.00726621
[2023-09-01 22:54:08.445] [jointLog] [info] Finished optimizer
[2023-09-01 22:54:08.445] [jointLog] [info] writing output