[2023-09-01 19:13:12.845] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-01 19:13:12.845] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-01 19:13:12.845] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-01 19:13:12.845] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-01 19:13:12.845] [jointLog] [info] parsing read library format
[2023-09-01 19:13:12.845] [jointLog] [info] There is 1 library.
[2023-09-01 19:13:12.845] [jointLog] [info] Loading pufferfish index
[2023-09-01 19:13:12.845] [jointLog] [info] Loading dense pufferfish index.
[2023-09-01 19:14:35.422] [jointLog] [info] done
[2023-09-01 19:14:35.581] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-01 19:15:15.333] [jointLog] [info] Number of decoys : 194
[2023-09-01 19:15:15.333] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-01 19:15:18.694] [jointLog] [info] Automatically detected most likely library type as ISF

[2023-09-01 19:23:20.981] [jointLog] [info] Thread saw mini-batch with a maximum of 5.32% zero probability fragments
[2023-09-01 19:23:20.983] [jointLog] [info] Thread saw mini-batch with a maximum of 5.00% zero probability fragments
[2023-09-01 19:23:20.985] [jointLog] [info] Thread saw mini-batch with a maximum of 5.26% zero probability fragments
[2023-09-01 19:23:20.991] [jointLog] [info] Thread saw mini-batch with a maximum of 5.04% zero probability fragments
[2023-09-01 19:23:21.041] [jointLog] [info] Thread saw mini-batch with a maximum of 5.02% zero probability fragments
[2023-09-01 19:23:21.149] [jointLog] [info] Thread saw mini-batch with a maximum of 5.14% zero probability fragments
[2023-09-01 19:23:21.163] [jointLog] [info] Thread saw mini-batch with a maximum of 5.04% zero probability fragments
[2023-09-01 19:23:21.166] [jointLog] [info] Thread saw mini-batch with a maximum of 5.08% zero probability fragments
[2023-09-01 19:23:21.679] [jointLog] [info] Computed 228,029 rich equivalence classes for further processing
[2023-09-01 19:23:21.679] [jointLog] [info] Counted 19,892,313 total reads in the equivalence classes 
[2023-09-01 19:23:21.691] [jointLog] [info] Number of mappings discarded because of alignment score : 16,471,840
[2023-09-01 19:23:21.691] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,926,089
[2023-09-01 19:23:21.691] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 1,031,886
[2023-09-01 19:23:21.691] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 467,690
[2023-09-01 19:23:21.691] [jointLog] [info] Mapping rate = 81.9765%

[2023-09-01 19:23:21.691] [jointLog] [info] finished quantifyLibrary()
[2023-09-01 19:23:21.691] [jointLog] [info] Starting optimizer
[2023-09-01 19:23:21.680] [fileLog] [info] 
At end of round 0
==================
Observed 24265858 total fragments (24265858 in most recent round)

[2023-09-01 19:23:27.791] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-01 19:23:28.123] [jointLog] [info] iteration = 0 | max rel diff. = 291.175
[2023-09-01 19:23:31.453] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-01 19:28:09.719] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-01 19:28:09.720] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-01 19:28:32.552] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-01 19:28:54.692] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-01 19:29:16.606] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-01 19:29:39.070] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-01 19:30:01.117] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-01 19:30:23.288] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-01 19:30:45.668] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-01 19:31:07.282] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-01 19:31:29.827] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-01 19:31:53.279] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-01 19:32:23.378] [jointLog] [info] iteration = 100 | max rel diff. = 10.6731
[2023-09-01 19:32:56.458] [jointLog] [info] iteration = 200 | max rel diff. = 14.656
[2023-09-01 19:33:30.252] [jointLog] [info] iteration = 300 | max rel diff. = 3.25565
[2023-09-01 19:34:04.144] [jointLog] [info] iteration = 400 | max rel diff. = 0.253525
[2023-09-01 19:34:37.618] [jointLog] [info] iteration = 500 | max rel diff. = 0.338312
[2023-09-01 19:35:10.879] [jointLog] [info] iteration = 600 | max rel diff. = 0.0728492
[2023-09-01 19:35:44.878] [jointLog] [info] iteration = 700 | max rel diff. = 0.133074
[2023-09-01 19:36:18.823] [jointLog] [info] iteration = 800 | max rel diff. = 0.132511
[2023-09-01 19:36:53.072] [jointLog] [info] iteration = 900 | max rel diff. = 0.0970443
[2023-09-01 19:37:26.973] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.294456
[2023-09-01 19:38:01.271] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.131914
[2023-09-01 19:38:23.365] [jointLog] [info] iteration = 1,165 | max rel diff. = 0.00888663
[2023-09-01 19:38:25.257] [jointLog] [info] Finished optimizer
[2023-09-01 19:38:25.257] [jointLog] [info] writing output