[2021-08-11 18:12:41.220] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-11 18:12:41.220] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-11 18:12:41.220] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-11 18:12:41.220] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-11 18:12:41.220] [jointLog] [info] parsing read library format
[2021-08-11 18:12:41.220] [jointLog] [info] There is 1 library.
[2021-08-11 18:12:41.338] [jointLog] [info] Loading pufferfish index
[2021-08-11 18:12:41.338] [jointLog] [info] Loading dense pufferfish index.
[2021-08-11 18:14:28.059] [jointLog] [info] done
[2021-08-11 18:14:28.059] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-11 18:15:19.649] [jointLog] [info] Number of decoys : 194
[2021-08-11 18:15:19.649] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-11 18:15:21.092] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-11 18:15:21.992] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-11 18:15:58.422] [jointLog] [info] Thread saw mini-batch with a maximum of 5.02% zero probability fragments
[2021-08-11 18:15:58.439] [jointLog] [info] Thread saw mini-batch with a maximum of 4.88% zero probability fragments
[2021-08-11 18:15:58.479] [jointLog] [info] Thread saw mini-batch with a maximum of 4.84% zero probability fragments
[2021-08-11 18:15:58.505] [jointLog] [info] Thread saw mini-batch with a maximum of 4.90% zero probability fragments
[2021-08-11 18:15:58.518] [jointLog] [info] Thread saw mini-batch with a maximum of 4.76% zero probability fragments
[2021-08-11 18:15:58.518] [jointLog] [info] Thread saw mini-batch with a maximum of 4.96% zero probability fragments
[2021-08-11 18:15:58.518] [jointLog] [info] Thread saw mini-batch with a maximum of 4.78% zero probability fragments
[2021-08-11 18:15:58.535] [jointLog] [info] Thread saw mini-batch with a maximum of 4.92% zero probability fragments
[2021-08-11 18:15:58.695] [jointLog] [info] Computed 164,919 rich equivalence classes for further processing
[2021-08-11 18:15:58.695] [jointLog] [info] Counted 5,756,878 total reads in the equivalence classes 
[2021-08-11 18:15:58.705] [jointLog] [info] Number of mappings discarded because of alignment score : 8,075,360
[2021-08-11 18:15:58.705] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 144,791
[2021-08-11 18:15:58.705] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 92,592
[2021-08-11 18:15:58.705] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-11 18:15:58.705] [jointLog] [info] Mapping rate = 91.2593%

[2021-08-11 18:15:58.705] [jointLog] [info] finished quantifyLibrary()
[2021-08-11 18:15:58.705] [jointLog] [info] Starting optimizer
[2021-08-11 18:15:58.696] [fileLog] [info] 
At end of round 0
==================
Observed 6308263 total fragments (6308263 in most recent round)

[2021-08-11 18:16:01.789] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-11 18:16:02.114] [jointLog] [info] iteration = 0 | max rel diff. = 139.695
[2021-08-11 18:16:05.384] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-11 18:16:59.601] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-11 18:16:59.601] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-11 18:17:04.690] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-11 18:17:09.571] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-11 18:17:14.871] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-11 18:17:19.774] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-11 18:17:24.849] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-11 18:17:29.934] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-11 18:17:35.149] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-11 18:17:40.116] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-11 18:17:45.225] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-11 18:17:50.372] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-11 18:18:20.237] [jointLog] [info] iteration = 100 | max rel diff. = 18.0512
[2021-08-11 18:18:53.153] [jointLog] [info] iteration = 200 | max rel diff. = 2.34607
[2021-08-11 18:19:24.476] [jointLog] [info] iteration = 300 | max rel diff. = 9.8928
[2021-08-11 18:19:55.768] [jointLog] [info] iteration = 400 | max rel diff. = 1.0583
[2021-08-11 18:20:27.078] [jointLog] [info] iteration = 500 | max rel diff. = 0.273314
[2021-08-11 18:20:58.326] [jointLog] [info] iteration = 600 | max rel diff. = 0.110994
[2021-08-11 18:21:29.511] [jointLog] [info] iteration = 700 | max rel diff. = 0.349116
[2021-08-11 18:22:00.780] [jointLog] [info] iteration = 800 | max rel diff. = 0.0639754
[2021-08-11 18:22:32.041] [jointLog] [info] iteration = 900 | max rel diff. = 0.298664
[2021-08-11 18:23:03.209] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.053521
[2021-08-11 18:23:34.448] [jointLog] [info] iteration = 1,100 | max rel diff. = 1.51558
[2021-08-11 18:23:39.785] [jointLog] [info] iteration = 1,118 | max rel diff. = 0.00595361
[2021-08-11 18:23:41.388] [jointLog] [info] Finished optimizer
[2021-08-11 18:23:41.388] [jointLog] [info] writing output