[2023-09-20 00:57:55.121] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 00:57:55.121] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 00:57:55.121] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 00:57:55.121] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 00:57:55.121] [jointLog] [info] parsing read library format
[2023-09-20 00:57:55.122] [jointLog] [info] There is 1 library.
[2023-09-20 00:57:55.122] [jointLog] [info] Loading pufferfish index
[2023-09-20 00:57:55.122] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 00:59:13.454] [jointLog] [info] done
[2023-09-20 00:59:13.626] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 00:59:54.385] [jointLog] [info] Number of decoys : 194
[2023-09-20 00:59:54.385] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 00:59:56.592] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 00:59:57.982] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 01:00:38.773] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-20 01:00:38.803] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-09-20 01:00:38.919] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-09-20 01:00:39.021] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-20 01:00:39.034] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-20 01:00:39.108] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-20 01:00:39.114] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-20 01:00:39.147] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-20 01:00:39.356] [jointLog] [info] Computed 79,925 rich equivalence classes for further processing
[2023-09-20 01:00:39.356] [jointLog] [info] Counted 1,845,803 total reads in the equivalence classes 
[2023-09-20 01:00:39.364] [jointLog] [info] Number of mappings discarded because of alignment score : 56,406,063
[2023-09-20 01:00:39.364] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 296,740
[2023-09-20 01:00:39.364] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 51,938
[2023-09-20 01:00:39.364] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 01:00:39.357] [fileLog] [info] 
At end of round 0
==================
Observed 2497872 total fragments (2497872 in most recent round)

[2023-09-20 01:00:41.110] [jointLog] [warning] Only 1845803 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-20 01:00:41.110] [jointLog] [info] Mapping rate = 73.895%

[2023-09-20 01:00:41.110] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 01:00:41.111] [jointLog] [info] Starting optimizer
[2023-09-20 01:00:46.462] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 01:00:46.815] [jointLog] [info] iteration = 0 | max rel diff. = 37.3944
[2023-09-20 01:00:50.335] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 01:01:41.753] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 01:01:41.754] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 01:01:46.840] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 01:01:51.715] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 01:01:56.515] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 01:02:01.824] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 01:02:06.682] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 01:02:11.406] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 01:02:16.708] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 01:02:21.666] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 01:02:26.539] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 01:02:31.404] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 01:03:04.192] [jointLog] [info] iteration = 100 | max rel diff. = 3.03519
[2023-09-20 01:03:40.161] [jointLog] [info] iteration = 200 | max rel diff. = 0.82388
[2023-09-20 01:04:16.121] [jointLog] [info] iteration = 300 | max rel diff. = 0.150309
[2023-09-20 01:04:52.042] [jointLog] [info] iteration = 400 | max rel diff. = 0.104617
[2023-09-20 01:05:28.565] [jointLog] [info] iteration = 500 | max rel diff. = 0.111756
[2023-09-20 01:06:05.059] [jointLog] [info] iteration = 600 | max rel diff. = 0.010473
[2023-09-20 01:06:41.449] [jointLog] [info] iteration = 700 | max rel diff. = 0.0138904
[2023-09-20 01:07:17.845] [jointLog] [info] iteration = 800 | max rel diff. = 0.0319212
[2023-09-20 01:07:43.860] [jointLog] [info] iteration = 873 | max rel diff. = 0.00592349
[2023-09-20 01:07:46.347] [jointLog] [info] Finished optimizer
[2023-09-20 01:07:46.347] [jointLog] [info] writing output