[2023-09-21 04:15:54.646] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-21 04:15:54.646] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-21 04:15:54.646] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-21 04:15:54.646] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-21 04:15:54.646] [jointLog] [info] parsing read library format
[2023-09-21 04:15:54.646] [jointLog] [info] There is 1 library.
[2023-09-21 04:15:54.646] [jointLog] [info] Loading pufferfish index
[2023-09-21 04:15:54.646] [jointLog] [info] Loading dense pufferfish index.
[2023-09-21 04:17:06.691] [jointLog] [info] done
[2023-09-21 04:17:06.874] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-21 04:17:48.341] [jointLog] [info] Number of decoys : 194
[2023-09-21 04:17:48.341] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-21 04:17:50.886] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-21 04:17:51.981] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-21 04:18:37.080] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-21 04:18:37.154] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-21 04:18:37.203] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-21 04:18:37.271] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-21 04:18:37.338] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-09-21 04:18:37.374] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-21 04:18:37.546] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-21 04:18:37.565] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-21 04:18:37.786] [fileLog] [info] 
At end of round 0
==================
Observed 2967959 total fragments (2967959 in most recent round)

[2023-09-21 04:18:37.785] [jointLog] [info] Computed 88,098 rich equivalence classes for further processing
[2023-09-21 04:18:37.785] [jointLog] [info] Counted 2,130,618 total reads in the equivalence classes 
[2023-09-21 04:18:37.794] [jointLog] [info] Number of mappings discarded because of alignment score : 58,847,055
[2023-09-21 04:18:37.794] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 370,988
[2023-09-21 04:18:37.794] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,036
[2023-09-21 04:18:37.794] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-21 04:18:39.427] [jointLog] [warning] Only 2130618 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 04:18:39.427] [jointLog] [info] Mapping rate = 71.7873%

[2023-09-21 04:18:39.427] [jointLog] [info] finished quantifyLibrary()
[2023-09-21 04:18:39.428] [jointLog] [info] Starting optimizer
[2023-09-21 04:18:44.874] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-21 04:18:45.221] [jointLog] [info] iteration = 0 | max rel diff. = 39.4264
[2023-09-21 04:18:48.703] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-21 04:19:41.442] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-21 04:19:41.443] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-21 04:19:46.293] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-21 04:19:51.295] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-21 04:19:56.103] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-21 04:20:01.022] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-21 04:20:05.497] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-21 04:20:10.517] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-21 04:20:15.224] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-21 04:20:20.040] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-21 04:20:25.105] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-21 04:20:29.846] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-21 04:21:02.735] [jointLog] [info] iteration = 100 | max rel diff. = 19.2991
[2023-09-21 04:21:38.617] [jointLog] [info] iteration = 200 | max rel diff. = 7.30485
[2023-09-21 04:22:14.301] [jointLog] [info] iteration = 300 | max rel diff. = 0.170539
[2023-09-21 04:22:49.826] [jointLog] [info] iteration = 400 | max rel diff. = 0.0400488
[2023-09-21 04:23:25.303] [jointLog] [info] iteration = 500 | max rel diff. = 4.10552
[2023-09-21 04:24:00.634] [jointLog] [info] iteration = 600 | max rel diff. = 11.841
[2023-09-21 04:24:35.986] [jointLog] [info] iteration = 700 | max rel diff. = 1.24191
[2023-09-21 04:25:11.486] [jointLog] [info] iteration = 800 | max rel diff. = 0.0299004
[2023-09-21 04:25:23.894] [jointLog] [info] iteration = 836 | max rel diff. = 0.00119333
[2023-09-21 04:25:26.424] [jointLog] [info] Finished optimizer
[2023-09-21 04:25:26.424] [jointLog] [info] writing output