[2023-09-21 14:13:46.220] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 14:13:46.220] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 14:13:46.221] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 14:13:46.221] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 14:13:46.221] [jointLog] [info] parsing read library format
[2023-09-21 14:13:46.221] [jointLog] [info] There is 1 library.
[2023-09-21 14:13:46.221] [jointLog] [info] Loading pufferfish index
[2023-09-21 14:13:46.221] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 14:15:01.421] [jointLog] [info] done
[2023-09-21 14:15:01.549] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 14:15:39.111] [jointLog] [info] Number of decoys : 194
[2023-09-21 14:15:39.111] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 14:15:41.022] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 14:15:42.073] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 14:16:38.804] [jointLog] [info] Thread saw mini-batch with a maximum of 2.54% zero probability fragments
[2023-09-21 14:16:38.822] [jointLog] [info] Thread saw mini-batch with a maximum of 2.58% zero probability fragments
[2023-09-21 14:16:38.835] [jointLog] [info] Thread saw mini-batch with a maximum of 2.64% zero probability fragments
[2023-09-21 14:16:38.885] [jointLog] [info] Thread saw mini-batch with a maximum of 2.64% zero probability fragments
[2023-09-21 14:16:38.911] [jointLog] [info] Thread saw mini-batch with a maximum of 2.64% zero probability fragments
[2023-09-21 14:16:38.944] [jointLog] [info] Thread saw mini-batch with a maximum of 2.42% zero probability fragments
[2023-09-21 14:16:38.944] [jointLog] [info] Thread saw mini-batch with a maximum of 2.58% zero probability fragments
[2023-09-21 14:16:39.416] [fileLog] [info] 
At end of round 0
==================
Observed 4056659 total fragments (4056659 in most recent round)

[2023-09-21 14:16:39.240] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-09-21 14:16:39.415] [jointLog] [info] Computed 94,714 rich equivalence classes for further processing
[2023-09-21 14:16:39.415] [jointLog] [info] Counted 2,480,056 total reads in the equivalence classes 
[2023-09-21 14:16:39.422] [jointLog] [info] Number of mappings discarded because of alignment score : 65,654,827
[2023-09-21 14:16:39.422] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 370,877
[2023-09-21 14:16:39.423] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 75,576
[2023-09-21 14:16:39.423] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 14:16:40.393] [jointLog] [warning] Only 2480056 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 14:16:40.393] [jointLog] [info] Mapping rate = 61.1354%

[2023-09-21 14:16:40.393] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 14:16:40.394] [jointLog] [info] Starting optimizer
[2023-09-21 14:16:44.390] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 14:16:44.725] [jointLog] [info] iteration = 0 | max rel diff. = 86.9872
[2023-09-21 14:16:48.126] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 14:17:46.199] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 14:17:46.199] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 14:17:51.224] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 14:17:56.561] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 14:18:01.711] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 14:18:06.968] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 14:18:12.207] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 14:18:17.652] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 14:18:23.165] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 14:18:28.689] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 14:18:33.833] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 14:18:39.331] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 14:19:09.740] [jointLog] [info] iteration = 100 | max rel diff. = 15.1895
[2023-09-21 14:19:43.473] [jointLog] [info] iteration = 200 | max rel diff. = 1.50865
[2023-09-21 14:20:17.113] [jointLog] [info] iteration = 300 | max rel diff. = 2.61297
[2023-09-21 14:20:50.896] [jointLog] [info] iteration = 400 | max rel diff. = 0.322747
[2023-09-21 14:21:24.814] [jointLog] [info] iteration = 500 | max rel diff. = 0.114299
[2023-09-21 14:21:58.164] [jointLog] [info] iteration = 600 | max rel diff. = 0.563469
[2023-09-21 14:22:31.147] [jointLog] [info] iteration = 700 | max rel diff. = 0.60274
[2023-09-21 14:23:04.216] [jointLog] [info] iteration = 800 | max rel diff. = 0.455882
[2023-09-21 14:23:05.189] [jointLog] [info] iteration = 804 | max rel diff. = 0.00207684
[2023-09-21 14:23:07.142] [jointLog] [info] Finished optimizer
[2023-09-21 14:23:07.143] [jointLog] [info] writing output