[2023-09-17 09:35:10.142] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-17 09:35:10.142] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-17 09:35:10.142] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-17 09:35:10.142] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-17 09:35:10.142] [jointLog] [info] parsing read library format
[2023-09-17 09:35:10.142] [jointLog] [info] There is 1 library.
[2023-09-17 09:35:10.142] [jointLog] [info] Loading pufferfish index
[2023-09-17 09:35:10.142] [jointLog] [info] Loading dense pufferfish index.
[2023-09-17 09:36:25.909] [jointLog] [info] done
[2023-09-17 09:36:26.082] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-17 09:37:06.373] [jointLog] [info] Number of decoys : 194
[2023-09-17 09:37:06.373] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-17 09:37:08.669] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-17 09:37:09.233] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-17 09:37:47.423] [jointLog] [info] Thread saw mini-batch with a maximum of 4.64% zero probability fragments
[2023-09-17 09:37:47.425] [jointLog] [info] Thread saw mini-batch with a maximum of 4.14% zero probability fragments
[2023-09-17 09:37:47.437] [jointLog] [info] Thread saw mini-batch with a maximum of 4.28% zero probability fragments
[2023-09-17 09:37:47.437] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-09-17 09:37:47.445] [jointLog] [info] Thread saw mini-batch with a maximum of 4.22% zero probability fragments
[2023-09-17 09:37:47.456] [jointLog] [info] Thread saw mini-batch with a maximum of 4.12% zero probability fragments
[2023-09-17 09:37:47.480] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2023-09-17 09:37:47.502] [jointLog] [info] Thread saw mini-batch with a maximum of 4.22% zero probability fragments
[2023-09-17 09:37:47.765] [jointLog] [info] Computed 209,966 rich equivalence classes for further processing
[2023-09-17 09:37:47.765] [jointLog] [info] Counted 5,846,138 total reads in the equivalence classes 
[2023-09-17 09:37:47.773] [jointLog] [info] Number of mappings discarded because of alignment score : 9,737,367
[2023-09-17 09:37:47.773] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 59,230
[2023-09-17 09:37:47.773] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 41,659
[2023-09-17 09:37:47.773] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-17 09:37:47.773] [jointLog] [info] Mapping rate = 91.3144%

[2023-09-17 09:37:47.773] [jointLog] [info] finished quantifyLibrary()
[2023-09-17 09:37:47.774] [jointLog] [info] Starting optimizer
[2023-09-17 09:37:47.765] [fileLog] [info] 
At end of round 0
==================
Observed 6402211 total fragments (6402211 in most recent round)

[2023-09-17 09:37:53.115] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-17 09:37:53.480] [jointLog] [info] iteration = 0 | max rel diff. = 135.874
[2023-09-17 09:37:57.006] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-17 09:39:06.994] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-17 09:39:06.994] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-17 09:39:13.146] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-17 09:39:19.465] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-17 09:39:25.934] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-17 09:39:32.494] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-17 09:39:38.863] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-17 09:39:45.530] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-17 09:39:51.810] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-17 09:39:58.370] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-17 09:40:04.700] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-17 09:40:11.349] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-17 09:40:11.350] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-17 09:40:46.568] [jointLog] [info] iteration = 100 | max rel diff. = 15.9031
[2023-09-17 09:41:22.474] [jointLog] [info] iteration = 200 | max rel diff. = 8.87122
[2023-09-17 09:41:59.520] [jointLog] [info] iteration = 300 | max rel diff. = 4.89294
[2023-09-17 09:42:35.757] [jointLog] [info] iteration = 400 | max rel diff. = 6.86178
[2023-09-17 09:43:12.860] [jointLog] [info] iteration = 500 | max rel diff. = 4.4395
[2023-09-17 09:43:48.871] [jointLog] [info] iteration = 600 | max rel diff. = 0.429543
[2023-09-17 09:44:24.600] [jointLog] [info] iteration = 700 | max rel diff. = 0.936348
[2023-09-17 09:45:00.121] [jointLog] [info] iteration = 800 | max rel diff. = 3.41042
[2023-09-17 09:45:35.805] [jointLog] [info] iteration = 900 | max rel diff. = 0.116249
[2023-09-17 09:46:12.177] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0657554
[2023-09-17 09:46:48.705] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0840898
[2023-09-17 09:47:25.067] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0610838
[2023-09-17 09:48:01.857] [jointLog] [info] iteration = 1,300 | max rel diff. = 1.06308
[2023-09-17 09:48:38.301] [jointLog] [info] iteration = 1,400 | max rel diff. = 2.95908
[2023-09-17 09:48:46.215] [jointLog] [info] iteration = 1,422 | max rel diff. = 0.0098367
[2023-09-17 09:48:49.019] [jointLog] [info] Finished optimizer
[2023-09-17 09:48:49.019] [jointLog] [info] writing output