[2023-08-25 12:42:40.825] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 12:42:40.825] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 12:42:40.825] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 12:42:40.826] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 12:42:40.826] [jointLog] [info] parsing read library format
[2023-08-25 12:42:40.826] [jointLog] [info] There is 1 library.
[2023-08-25 12:42:40.826] [jointLog] [info] Loading pufferfish index
[2023-08-25 12:42:40.826] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 12:43:59.289] [jointLog] [info] done
[2023-08-25 12:43:59.409] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 12:44:34.857] [jointLog] [info] Number of decoys : 194
[2023-08-25 12:44:34.857] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 12:44:37.043] [jointLog] [info] Automatically detected most likely library type as IU

[2023-08-25 12:51:23.200] [jointLog] [info] Computed 318,643 rich equivalence classes for further processing
[2023-08-25 12:51:23.200] [jointLog] [info] Counted 26,490,825 total reads in the equivalence classes 
[2023-08-25 12:51:23.210] [jointLog] [info] Number of mappings discarded because of alignment score : 14,402,602
[2023-08-25 12:51:23.210] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,344,100
[2023-08-25 12:51:23.210] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 639,787
[2023-08-25 12:51:23.210] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 874,544
[2023-08-25 12:51:23.210] [jointLog] [info] Mapping rate = 91.0218%

[2023-08-25 12:51:23.210] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 12:51:23.211] [jointLog] [info] Starting optimizer
[2023-08-25 12:51:23.201] [fileLog] [info] 
At end of round 0
==================
Observed 29103836 total fragments (29103836 in most recent round)

[2023-08-25 12:51:28.113] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 12:51:28.459] [jointLog] [info] iteration = 0 | max rel diff. = 300.398
[2023-08-25 12:51:32.029] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 12:55:49.814] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 12:55:49.814] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 12:56:10.350] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 12:56:31.512] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 12:56:53.100] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 12:57:15.951] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 12:57:36.801] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 12:57:58.039] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 12:58:19.273] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 12:58:39.495] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 12:58:59.649] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 12:59:21.440] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 12:59:21.443] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 12:59:52.867] [jointLog] [info] iteration = 100 | max rel diff. = 12.6164
[2023-08-25 13:00:28.955] [jointLog] [info] iteration = 200 | max rel diff. = 2.13206
[2023-08-25 13:01:04.294] [jointLog] [info] iteration = 300 | max rel diff. = 2.14509
[2023-08-25 13:01:39.947] [jointLog] [info] iteration = 400 | max rel diff. = 1.5522
[2023-08-25 13:02:15.024] [jointLog] [info] iteration = 500 | max rel diff. = 1.819
[2023-08-25 13:02:48.838] [jointLog] [info] iteration = 600 | max rel diff. = 0.0459572
[2023-08-25 13:03:22.759] [jointLog] [info] iteration = 700 | max rel diff. = 0.219571
[2023-08-25 13:03:56.499] [jointLog] [info] iteration = 800 | max rel diff. = 0.110105
[2023-08-25 13:04:30.243] [jointLog] [info] iteration = 900 | max rel diff. = 0.0357283
[2023-08-25 13:05:03.641] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.10195
[2023-08-25 13:05:37.076] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.230813
[2023-08-25 13:06:05.284] [jointLog] [info] iteration = 1,186 | max rel diff. = 0.00296673
[2023-08-25 13:06:07.803] [jointLog] [info] Finished optimizer
[2023-08-25 13:06:07.803] [jointLog] [info] writing output