[2021-08-01 03:14:12.618] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-01 03:14:12.618] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-01 03:14:12.618] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-01 03:14:12.618] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-01 03:14:12.618] [jointLog] [info] parsing read library format
[2021-08-01 03:14:12.618] [jointLog] [info] There is 1 library.
[2021-08-01 03:14:12.744] [jointLog] [info] Loading pufferfish index
[2021-08-01 03:14:12.744] [jointLog] [info] Loading dense pufferfish index.
[2021-08-01 03:15:59.078] [jointLog] [info] done
[2021-08-01 03:15:59.078] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-01 03:16:57.078] [jointLog] [info] Number of decoys : 194
[2021-08-01 03:16:57.078] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-01 03:16:58.532] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-01 03:16:59.471] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-01 03:17:17.635] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2021-08-01 03:17:17.639] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2021-08-01 03:17:17.665] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2021-08-01 03:17:17.678] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2021-08-01 03:17:17.688] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2021-08-01 03:17:17.714] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2021-08-01 03:17:17.763] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2021-08-01 03:17:17.792] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2021-08-01 03:17:17.938] [jointLog] [info] Computed 116,722 rich equivalence classes for further processing
[2021-08-01 03:17:17.938] [jointLog] [info] Counted 3,272,026 total reads in the equivalence classes 
[2021-08-01 03:17:17.951] [jointLog] [info] Number of mappings discarded because of alignment score : 4,328,543
[2021-08-01 03:17:17.951] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,623
[2021-08-01 03:17:17.951] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 17,183
[2021-08-01 03:17:17.951] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-01 03:17:17.939] [fileLog] [info] 
At end of round 0
==================
Observed 3476777 total fragments (3476777 in most recent round)

[2021-08-01 03:17:20.228] [jointLog] [warning] Only 3272026 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2021-08-01 03:17:20.228] [jointLog] [info] Mapping rate = 94.1109%

[2021-08-01 03:17:20.228] [jointLog] [info] finished quantifyLibrary()
[2021-08-01 03:17:20.228] [jointLog] [info] Starting optimizer
[2021-08-01 03:17:26.670] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-01 03:17:27.110] [jointLog] [info] iteration = 0 | max rel diff. = 74.3641
[2021-08-01 03:17:30.680] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-01 03:18:14.371] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-01 03:18:14.371] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-01 03:18:18.253] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-01 03:18:22.434] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-01 03:18:26.638] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-01 03:18:30.731] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-01 03:18:34.709] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-01 03:18:39.012] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-01 03:18:42.955] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-01 03:18:46.999] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-01 03:18:51.104] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-01 03:18:55.378] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-01 03:19:28.541] [jointLog] [info] iteration = 100 | max rel diff. = 15.3591
[2021-08-01 03:20:03.846] [jointLog] [info] iteration = 200 | max rel diff. = 15.6105
[2021-08-01 03:20:38.821] [jointLog] [info] iteration = 300 | max rel diff. = 1.28798
[2021-08-01 03:21:13.360] [jointLog] [info] iteration = 400 | max rel diff. = 0.942151
[2021-08-01 03:21:48.282] [jointLog] [info] iteration = 500 | max rel diff. = 10.7507
[2021-08-01 03:22:22.467] [jointLog] [info] iteration = 600 | max rel diff. = 0.456094
[2021-08-01 03:22:56.689] [jointLog] [info] iteration = 700 | max rel diff. = 0.0839631
[2021-08-01 03:23:31.115] [jointLog] [info] iteration = 800 | max rel diff. = 1.56716
[2021-08-01 03:24:06.018] [jointLog] [info] iteration = 900 | max rel diff. = 0.0667933
[2021-08-01 03:24:41.488] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.048907
[2021-08-01 03:25:15.436] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.18631
[2021-08-01 03:25:30.584] [jointLog] [info] iteration = 1,146 | max rel diff. = 0.00513023
[2021-08-01 03:25:32.645] [jointLog] [info] Finished optimizer
[2021-08-01 03:25:32.645] [jointLog] [info] writing output