[2023-09-16 05:25:12.330] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-16 05:25:12.330] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-16 05:25:12.330] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-16 05:25:12.330] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-16 05:25:12.330] [jointLog] [info] parsing read library format
[2023-09-16 05:25:12.330] [jointLog] [info] There is 1 library.
[2023-09-16 05:25:12.330] [jointLog] [info] Loading pufferfish index
[2023-09-16 05:25:12.330] [jointLog] [info] Loading dense pufferfish index.
[2023-09-16 05:26:25.956] [jointLog] [info] done
[2023-09-16 05:26:26.118] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-16 05:27:04.850] [jointLog] [info] Number of decoys : 194
[2023-09-16 05:27:04.850] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-16 05:27:06.926] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-16 05:27:07.516] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-16 05:27:54.606] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-09-16 05:27:54.675] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-09-16 05:27:54.693] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-09-16 05:27:54.707] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-09-16 05:27:54.721] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-09-16 05:27:54.778] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-09-16 05:27:54.804] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-09-16 05:27:54.804] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-16 05:27:55.101] [jointLog] [info] Computed 172,337 rich equivalence classes for further processing
[2023-09-16 05:27:55.101] [jointLog] [info] Counted 6,079,754 total reads in the equivalence classes 
[2023-09-16 05:27:55.111] [jointLog] [info] Number of mappings discarded because of alignment score : 11,458,479
[2023-09-16 05:27:55.111] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 124,693
[2023-09-16 05:27:55.111] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 68,417
[2023-09-16 05:27:55.111] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-16 05:27:55.111] [jointLog] [info] Mapping rate = 91.6665%

[2023-09-16 05:27:55.111] [jointLog] [info] finished quantifyLibrary()
[2023-09-16 05:27:55.111] [jointLog] [info] Starting optimizer
[2023-09-16 05:27:55.102] [fileLog] [info] 
At end of round 0
==================
Observed 6632469 total fragments (6632469 in most recent round)

[2023-09-16 05:28:00.111] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-16 05:28:00.433] [jointLog] [info] iteration = 0 | max rel diff. = 119.195
[2023-09-16 05:28:03.748] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-16 05:29:10.929] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-16 05:29:10.929] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-16 05:29:16.866] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-16 05:29:22.998] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-16 05:29:29.436] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-16 05:29:35.727] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-16 05:29:41.994] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-16 05:29:48.416] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-16 05:29:54.477] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-16 05:30:00.489] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-16 05:30:06.890] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-16 05:30:12.888] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 05:30:44.599] [jointLog] [info] iteration = 100 | max rel diff. = 19.9474
[2023-09-16 05:31:18.555] [jointLog] [info] iteration = 200 | max rel diff. = 4.03245
[2023-09-16 05:31:53.852] [jointLog] [info] iteration = 300 | max rel diff. = 2.52753
[2023-09-16 05:32:27.704] [jointLog] [info] iteration = 400 | max rel diff. = 0.711737
[2023-09-16 05:33:00.827] [jointLog] [info] iteration = 500 | max rel diff. = 1.3727
[2023-09-16 05:33:35.651] [jointLog] [info] iteration = 600 | max rel diff. = 0.260021
[2023-09-16 05:34:08.664] [jointLog] [info] iteration = 700 | max rel diff. = 0.126553
[2023-09-16 05:34:40.514] [jointLog] [info] iteration = 800 | max rel diff. = 0.042252
[2023-09-16 05:35:12.495] [jointLog] [info] iteration = 900 | max rel diff. = 0.041206
[2023-09-16 05:35:44.329] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0348836
[2023-09-16 05:36:02.081] [jointLog] [info] iteration = 1,056 | max rel diff. = 0.008655
[2023-09-16 05:36:04.252] [jointLog] [info] Finished optimizer
[2023-09-16 05:36:04.252] [jointLog] [info] writing output