[2023-08-25 05:39:23.247] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 05:39:23.247] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 05:39:23.247] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 05:39:23.247] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 05:39:23.247] [jointLog] [info] parsing read library format
[2023-08-25 05:39:23.247] [jointLog] [info] There is 1 library.
[2023-08-25 05:39:23.247] [jointLog] [info] Loading pufferfish index
[2023-08-25 05:39:23.247] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 05:46:45.285] [jointLog] [info] done
[2023-08-25 05:46:46.207] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 05:50:18.539] [jointLog] [info] Number of decoys : 194
[2023-08-25 05:50:18.539] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 05:50:31.791] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 05:50:39.168] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 06:15:32.473] [jointLog] [info] Thread saw mini-batch with a maximum of 6.66% zero probability fragments
[2023-08-25 06:15:32.799] [jointLog] [info] Thread saw mini-batch with a maximum of 6.62% zero probability fragments
[2023-08-25 06:15:32.960] [jointLog] [info] Thread saw mini-batch with a maximum of 6.52% zero probability fragments
[2023-08-25 06:15:33.300] [jointLog] [info] Thread saw mini-batch with a maximum of 6.70% zero probability fragments
[2023-08-25 06:15:33.318] [jointLog] [info] Thread saw mini-batch with a maximum of 6.46% zero probability fragments
[2023-08-25 06:15:34.091] [jointLog] [info] Thread saw mini-batch with a maximum of 6.80% zero probability fragments
[2023-08-25 06:15:35.433] [jointLog] [info] Thread saw mini-batch with a maximum of 6.48% zero probability fragments
[2023-08-25 06:15:35.681] [jointLog] [info] Thread saw mini-batch with a maximum of 6.46% zero probability fragments
[2023-08-25 06:15:37.058] [fileLog] [info] 
At end of round 0
==================
Observed 23694932 total fragments (23694932 in most recent round)

[2023-08-25 06:15:37.057] [jointLog] [info] Computed 312,942 rich equivalence classes for further processing
[2023-08-25 06:15:37.057] [jointLog] [info] Counted 21,008,890 total reads in the equivalence classes 
[2023-08-25 06:15:37.072] [jointLog] [info] Number of mappings discarded because of alignment score : 40,800,146
[2023-08-25 06:15:37.072] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 607,828
[2023-08-25 06:15:37.072] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 315,290
[2023-08-25 06:15:37.072] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 06:15:37.072] [jointLog] [info] Mapping rate = 88.6641%

[2023-08-25 06:15:37.072] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 06:15:37.072] [jointLog] [info] Starting optimizer
[2023-08-25 06:20:17.155] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 06:20:19.301] [jointLog] [info] iteration = 0 | max rel diff. = 293.44
[2023-08-25 06:20:45.709] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 06:29:37.321] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 06:29:37.322] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 06:30:35.624] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 06:31:40.965] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 06:32:41.824] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 06:33:41.949] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 06:34:47.552] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 06:35:50.708] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 06:36:51.490] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 06:37:57.249] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 06:38:52.413] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 06:39:55.200] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 06:43:37.374] [jointLog] [info] iteration = 100 | max rel diff. = 16.9823
[2023-08-25 06:47:55.352] [jointLog] [info] iteration = 200 | max rel diff. = 2.8884
[2023-08-25 06:52:00.683] [jointLog] [info] iteration = 300 | max rel diff. = 3.40395
[2023-08-25 06:56:15.328] [jointLog] [info] iteration = 400 | max rel diff. = 4.23828
[2023-08-25 07:00:27.874] [jointLog] [info] iteration = 500 | max rel diff. = 10.1818
[2023-08-25 07:04:48.584] [jointLog] [info] iteration = 600 | max rel diff. = 0.982714
[2023-08-25 07:08:58.561] [jointLog] [info] iteration = 700 | max rel diff. = 0.176773
[2023-08-25 07:12:54.029] [jointLog] [info] iteration = 800 | max rel diff. = 0.326522
[2023-08-25 07:17:04.231] [jointLog] [info] iteration = 900 | max rel diff. = 0.115801
[2023-08-25 07:21:19.066] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.082141
[2023-08-25 07:25:43.943] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0666861
[2023-08-25 07:30:07.073] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.230137
[2023-08-25 07:34:33.896] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0155042
[2023-08-25 07:39:06.916] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.562872
[2023-08-25 07:43:32.063] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.180988
[2023-08-25 07:48:01.886] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.100344
[2023-08-25 07:49:03.532] [jointLog] [info] iteration = 1,625 | max rel diff. = 0.00683352
[2023-08-25 07:49:11.171] [jointLog] [info] Finished optimizer
[2023-08-25 07:49:11.171] [jointLog] [info] writing output