[2021-07-30 19:17:32.755] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-07-30 19:17:32.756] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-07-30 19:17:32.756] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-07-30 19:17:32.756] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-07-30 19:17:32.756] [jointLog] [info] parsing read library format
[2021-07-30 19:17:32.756] [jointLog] [info] There is 1 library.
[2021-07-30 19:17:32.879] [jointLog] [info] Loading pufferfish index
[2021-07-30 19:17:32.879] [jointLog] [info] Loading dense pufferfish index.
[2021-07-30 19:19:17.963] [jointLog] [info] done
[2021-07-30 19:19:17.963] [jointLog] [info] Index contained 5,382,683 targets
[2021-07-30 19:20:10.387] [jointLog] [info] Number of decoys : 194
[2021-07-30 19:20:10.387] [jointLog] [info] First decoy index : 5,185,409 
[2021-07-30 19:20:12.165] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-07-30 19:20:12.855] [jointLog] [info] Automatically detected most likely library type as SR
[2021-07-30 19:20:31.100] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2021-07-30 19:20:31.109] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2021-07-30 19:20:31.125] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2021-07-30 19:20:31.126] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2021-07-30 19:20:31.153] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2021-07-30 19:20:31.156] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2021-07-30 19:20:31.161] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2021-07-30 19:20:31.183] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2021-07-30 19:20:31.325] [jointLog] [info] Computed 122,765 rich equivalence classes for further processing
[2021-07-30 19:20:31.325] [jointLog] [info] Counted 3,691,437 total reads in the equivalence classes 
[2021-07-30 19:20:31.337] [jointLog] [info] Number of mappings discarded because of alignment score : 4,934,294
[2021-07-30 19:20:31.337] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 27,810
[2021-07-30 19:20:31.337] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 20,861
[2021-07-30 19:20:31.337] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-07-30 19:20:31.326] [fileLog] [info] 
At end of round 0
==================
Observed 3936722 total fragments (3936722 in most recent round)

[2021-07-30 19:20:32.837] [jointLog] [warning] Only 3691437 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2021-07-30 19:20:32.837] [jointLog] [info] Mapping rate = 93.7693%

[2021-07-30 19:20:32.837] [jointLog] [info] finished quantifyLibrary()
[2021-07-30 19:20:32.837] [jointLog] [info] Starting optimizer
[2021-07-30 19:20:36.971] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-07-30 19:20:37.302] [jointLog] [info] iteration = 0 | max rel diff. = 76.4193
[2021-07-30 19:20:40.677] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-07-30 19:21:24.053] [jointLog] [info] Computed expected counts (for bias correction)
[2021-07-30 19:21:24.054] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-07-30 19:21:27.987] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-07-30 19:21:32.074] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-07-30 19:21:36.135] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-07-30 19:21:40.453] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-07-30 19:21:44.441] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-07-30 19:21:48.522] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-07-30 19:21:52.810] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-07-30 19:21:56.613] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-07-30 19:22:00.595] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-07-30 19:22:05.325] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-07-30 19:22:37.304] [jointLog] [info] iteration = 100 | max rel diff. = 20.7242
[2021-07-30 19:23:12.959] [jointLog] [info] iteration = 200 | max rel diff. = 18.7671
[2021-07-30 19:23:48.461] [jointLog] [info] iteration = 300 | max rel diff. = 14.6773
[2021-07-30 19:24:23.952] [jointLog] [info] iteration = 400 | max rel diff. = 3.11702
[2021-07-30 19:24:59.523] [jointLog] [info] iteration = 500 | max rel diff. = 0.273445
[2021-07-30 19:25:35.196] [jointLog] [info] iteration = 600 | max rel diff. = 1.97801
[2021-07-30 19:26:10.863] [jointLog] [info] iteration = 700 | max rel diff. = 0.252317
[2021-07-30 19:26:46.567] [jointLog] [info] iteration = 800 | max rel diff. = 0.711356
[2021-07-30 19:27:22.236] [jointLog] [info] iteration = 900 | max rel diff. = 7.197
[2021-07-30 19:27:57.891] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0414063
[2021-07-30 19:28:17.803] [jointLog] [info] iteration = 1,057 | max rel diff. = 0.00775636
[2021-07-30 19:28:19.885] [jointLog] [info] Finished optimizer
[2021-07-30 19:28:19.885] [jointLog] [info] writing output