[2023-09-21 15:01:19.825] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 15:01:19.825] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 15:01:19.825] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 15:01:19.825] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 15:01:19.825] [jointLog] [info] parsing read library format
[2023-09-21 15:01:19.825] [jointLog] [info] There is 1 library.
[2023-09-21 15:01:19.826] [jointLog] [info] Loading pufferfish index
[2023-09-21 15:01:19.826] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 15:02:35.629] [jointLog] [info] done
[2023-09-21 15:02:35.750] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 15:03:12.456] [jointLog] [info] Number of decoys : 194
[2023-09-21 15:03:12.456] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 15:03:14.114] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 15:03:15.535] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 15:04:29.757] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-21 15:04:29.879] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-21 15:04:29.920] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-21 15:04:29.944] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-09-21 15:04:29.955] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-21 15:04:30.115] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-09-21 15:04:30.481] [fileLog] [info] 
At end of round 0
==================
Observed 3681312 total fragments (3681312 in most recent round)

[2023-09-21 15:04:30.331] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-21 15:04:30.337] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-21 15:04:30.481] [jointLog] [info] Computed 110,629 rich equivalence classes for further processing
[2023-09-21 15:04:30.481] [jointLog] [info] Counted 2,727,319 total reads in the equivalence classes 
[2023-09-21 15:04:30.487] [jointLog] [info] Number of mappings discarded because of alignment score : 110,576,744
[2023-09-21 15:04:30.487] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 430,750
[2023-09-21 15:04:30.487] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 94,586
[2023-09-21 15:04:30.487] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 15:04:31.334] [jointLog] [warning] Only 2727319 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-21 15:04:31.334] [jointLog] [info] Mapping rate = 74.0855%

[2023-09-21 15:04:31.334] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 15:04:31.335] [jointLog] [info] Starting optimizer
[2023-09-21 15:04:34.887] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 15:04:35.215] [jointLog] [info] iteration = 0 | max rel diff. = 61.918
[2023-09-21 15:04:38.549] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 15:05:42.446] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 15:05:42.446] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 15:05:48.880] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 15:05:54.710] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 15:06:00.579] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 15:06:06.702] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 15:06:12.522] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 15:06:18.606] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 15:06:24.422] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 15:06:30.118] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 15:06:36.056] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 15:06:41.805] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 15:06:41.808] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 15:07:11.458] [jointLog] [info] iteration = 100 | max rel diff. = 5.53883
[2023-09-21 15:07:44.513] [jointLog] [info] iteration = 200 | max rel diff. = 1.12607
[2023-09-21 15:08:17.157] [jointLog] [info] iteration = 300 | max rel diff. = 0.527225
[2023-09-21 15:08:51.273] [jointLog] [info] iteration = 400 | max rel diff. = 0.209931
[2023-09-21 15:09:24.653] [jointLog] [info] iteration = 500 | max rel diff. = 0.0680867
[2023-09-21 15:09:57.888] [jointLog] [info] iteration = 600 | max rel diff. = 0.359363
[2023-09-21 15:10:31.431] [jointLog] [info] iteration = 700 | max rel diff. = 0.0199586
[2023-09-21 15:11:04.139] [jointLog] [info] iteration = 800 | max rel diff. = 0.124541
[2023-09-21 15:11:24.593] [jointLog] [info] iteration = 863 | max rel diff. = 0.00697541
[2023-09-21 15:11:26.371] [jointLog] [info] Finished optimizer
[2023-09-21 15:11:26.371] [jointLog] [info] writing output