[2021-03-13 06:11:13.979] [jointLog] [info] setting maxHashResizeThreads to 12
[2021-03-13 06:11:13.979] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-13 06:11:13.979] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-13 06:11:13.979] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-13 06:11:13.979] [jointLog] [info] parsing read library format
[2021-03-13 06:11:13.979] [jointLog] [info] There is 1 library.
[2021-03-13 06:11:14.110] [jointLog] [info] Loading pufferfish index
[2021-03-13 06:11:14.110] [jointLog] [info] Loading dense pufferfish index.
[2021-03-13 06:12:52.553] [jointLog] [info] done
[2021-03-13 06:12:52.553] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-13 06:13:47.097] [jointLog] [info] Number of decoys : 194
[2021-03-13 06:13:47.098] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-13 06:13:48.417] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-13 06:13:49.133] [jointLog] [info] Automatically detected most likely library type as SR
[2021-03-13 06:14:05.895] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2021-03-13 06:14:05.895] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2021-03-13 06:14:05.900] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2021-03-13 06:14:05.903] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2021-03-13 06:14:05.915] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2021-03-13 06:14:05.923] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2021-03-13 06:14:05.940] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2021-03-13 06:14:05.998] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2021-03-13 06:14:06.009] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2021-03-13 06:14:06.062] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2021-03-13 06:14:06.082] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2021-03-13 06:14:06.117] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2021-03-13 06:14:06.297] [jointLog] [info] Computed 137,683 rich equivalence classes for further processing
[2021-03-13 06:14:06.297] [jointLog] [info] Counted 4,060,500 total reads in the equivalence classes 
[2021-03-13 06:14:06.314] [jointLog] [info] Number of mappings discarded because of alignment score : 4,417,096
[2021-03-13 06:14:06.314] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 69,500
[2021-03-13 06:14:06.314] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 37,715
[2021-03-13 06:14:06.314] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-13 06:14:06.297] [fileLog] [info] 
At end of round 0
==================
Observed 4325135 total fragments (4325135 in most recent round)

[2021-03-13 06:14:08.296] [jointLog] [warning] Only 4060500 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2021-03-13 06:14:08.296] [jointLog] [info] Mapping rate = 93.8815%

[2021-03-13 06:14:08.296] [jointLog] [info] finished quantifyLibrary()
[2021-03-13 06:14:08.297] [jointLog] [info] Starting optimizer
[2021-03-13 06:14:12.932] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-13 06:14:13.231] [jointLog] [info] iteration = 0 | max rel diff. = 75.0778
[2021-03-13 06:14:16.306] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-13 06:14:51.595] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-13 06:14:51.595] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-13 06:14:54.757] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-13 06:14:58.049] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-13 06:15:01.340] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-13 06:15:04.667] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-13 06:15:08.215] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-13 06:15:11.512] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-13 06:15:15.047] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-13 06:15:18.389] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-13 06:15:21.802] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-13 06:15:25.391] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-13 06:15:53.393] [jointLog] [info] iteration = 100 | max rel diff. = 5.83798
[2021-03-13 06:16:24.957] [jointLog] [info] iteration = 200 | max rel diff. = 10.236
[2021-03-13 06:16:56.918] [jointLog] [info] iteration = 300 | max rel diff. = 0.524109
[2021-03-13 06:17:28.563] [jointLog] [info] iteration = 400 | max rel diff. = 0.274235
[2021-03-13 06:18:00.297] [jointLog] [info] iteration = 500 | max rel diff. = 0.495629
[2021-03-13 06:18:31.664] [jointLog] [info] iteration = 600 | max rel diff. = 0.0982903
[2021-03-13 06:19:03.602] [jointLog] [info] iteration = 700 | max rel diff. = 0.103916
[2021-03-13 06:19:35.521] [jointLog] [info] iteration = 800 | max rel diff. = 4.3473
[2021-03-13 06:20:07.026] [jointLog] [info] iteration = 900 | max rel diff. = 0.0269316
[2021-03-13 06:20:38.393] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.80452
[2021-03-13 06:20:55.064] [jointLog] [info] iteration = 1,055 | max rel diff. = 0.00365854
[2021-03-13 06:20:57.260] [jointLog] [info] Finished optimizer
[2021-03-13 06:20:57.260] [jointLog] [info] writing output