[2023-10-04 00:02:15.766] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 00:02:15.766] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 00:02:15.766] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 00:02:15.766] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 00:02:15.767] [jointLog] [info] parsing read library format
[2023-10-04 00:02:15.767] [jointLog] [info] There is 1 library.
[2023-10-04 00:02:15.767] [jointLog] [info] Loading pufferfish index
[2023-10-04 00:02:15.767] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 00:03:34.700] [jointLog] [info] done
[2023-10-04 00:03:34.857] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 00:04:14.799] [jointLog] [info] Number of decoys : 194
[2023-10-04 00:04:14.799] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 00:04:16.659] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 00:04:17.241] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 00:05:05.630] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-04 00:05:05.646] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-10-04 00:05:05.707] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 00:05:05.731] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-04 00:05:05.761] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-04 00:05:05.903] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-04 00:05:05.907] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 00:05:05.982] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-04 00:05:06.154] [jointLog] [info] Computed 82,852 rich equivalence classes for further processing
[2023-10-04 00:05:06.154] [jointLog] [info] Counted 3,937,066 total reads in the equivalence classes 
[2023-10-04 00:05:06.163] [jointLog] [info] Number of mappings discarded because of alignment score : 47,563,064
[2023-10-04 00:05:06.163] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 365,714
[2023-10-04 00:05:06.163] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 120,809
[2023-10-04 00:05:06.163] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 00:05:06.155] [fileLog] [info] 
At end of round 0
==================
Observed 5103970 total fragments (5103970 in most recent round)

[2023-10-04 00:05:07.206] [jointLog] [warning] Only 3937066 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 00:05:07.206] [jointLog] [info] Mapping rate = 77.1373%

[2023-10-04 00:05:07.206] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 00:05:07.207] [jointLog] [info] Starting optimizer
[2023-10-04 00:05:12.430] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 00:05:12.776] [jointLog] [info] iteration = 0 | max rel diff. = 103.625
[2023-10-04 00:05:16.139] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 00:06:07.868] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 00:06:07.868] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 00:06:12.532] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 00:06:17.026] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 00:06:21.779] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 00:06:26.553] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 00:06:31.377] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 00:06:36.103] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 00:06:40.858] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 00:06:45.552] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 00:06:50.159] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 00:06:54.818] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 00:06:54.856] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 00:07:24.510] [jointLog] [info] iteration = 100 | max rel diff. = 16.2515
[2023-10-04 00:07:57.892] [jointLog] [info] iteration = 200 | max rel diff. = 0.392505
[2023-10-04 00:08:31.605] [jointLog] [info] iteration = 300 | max rel diff. = 0.723463
[2023-10-04 00:09:05.643] [jointLog] [info] iteration = 400 | max rel diff. = 1.20842
[2023-10-04 00:09:39.676] [jointLog] [info] iteration = 500 | max rel diff. = 0.418147
[2023-10-04 00:10:13.806] [jointLog] [info] iteration = 600 | max rel diff. = 0.0422896
[2023-10-04 00:10:46.082] [jointLog] [info] iteration = 700 | max rel diff. = 0.0748101
[2023-10-04 00:11:17.900] [jointLog] [info] iteration = 800 | max rel diff. = 0.0864663
[2023-10-04 00:11:43.330] [jointLog] [info] iteration = 881 | max rel diff. = 0.0090636
[2023-10-04 00:11:45.416] [jointLog] [info] Finished optimizer
[2023-10-04 00:11:45.416] [jointLog] [info] writing output