[2023-10-02 21:23:37.606] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 21:23:37.606] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 21:23:37.606] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 21:23:37.607] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 21:23:37.607] [jointLog] [info] parsing read library format
[2023-10-02 21:23:37.607] [jointLog] [info] There is 1 library.
[2023-10-02 21:23:37.607] [jointLog] [info] Loading pufferfish index
[2023-10-02 21:23:37.607] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 21:24:52.697] [jointLog] [info] done
[2023-10-02 21:24:52.854] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 21:25:33.511] [jointLog] [info] Number of decoys : 194
[2023-10-02 21:25:33.511] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 21:25:35.574] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 21:25:36.634] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 21:26:44.284] [jointLog] [info] Thread saw mini-batch with a maximum of 2.44% zero probability fragments
[2023-10-02 21:26:44.476] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-02 21:26:44.514] [jointLog] [info] Thread saw mini-batch with a maximum of 2.58% zero probability fragments
[2023-10-02 21:26:44.562] [jointLog] [info] Thread saw mini-batch with a maximum of 2.54% zero probability fragments
[2023-10-02 21:26:44.737] [jointLog] [info] Thread saw mini-batch with a maximum of 2.50% zero probability fragments
[2023-10-02 21:26:44.843] [jointLog] [info] Thread saw mini-batch with a maximum of 2.58% zero probability fragments
[2023-10-02 21:26:44.875] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-10-02 21:26:44.903] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-02 21:26:45.153] [fileLog] [info] 
At end of round 0
==================
Observed 4489786 total fragments (4489786 in most recent round)

[2023-10-02 21:26:45.152] [jointLog] [info] Computed 95,924 rich equivalence classes for further processing
[2023-10-02 21:26:45.152] [jointLog] [info] Counted 3,486,396 total reads in the equivalence classes 
[2023-10-02 21:26:45.176] [jointLog] [info] Number of mappings discarded because of alignment score : 56,807,659
[2023-10-02 21:26:45.176] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 402,965
[2023-10-02 21:26:45.176] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 88,198
[2023-10-02 21:26:45.176] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 21:26:46.281] [jointLog] [warning] Only 3486396 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-02 21:26:46.281] [jointLog] [info] Mapping rate = 77.6517%

[2023-10-02 21:26:46.281] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 21:26:46.281] [jointLog] [info] Starting optimizer
[2023-10-02 21:26:51.020] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 21:26:51.382] [jointLog] [info] iteration = 0 | max rel diff. = 85.3447
[2023-10-02 21:26:54.982] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 21:27:55.963] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 21:27:55.963] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 21:28:01.069] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 21:28:05.995] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 21:28:10.976] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 21:28:16.365] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 21:28:21.301] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 21:28:26.794] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 21:28:31.669] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 21:28:36.474] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 21:28:41.518] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 21:28:46.586] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 21:29:16.118] [jointLog] [info] iteration = 100 | max rel diff. = 3.8497
[2023-10-02 21:29:48.642] [jointLog] [info] iteration = 200 | max rel diff. = 5.20878
[2023-10-02 21:30:21.195] [jointLog] [info] iteration = 300 | max rel diff. = 0.920215
[2023-10-02 21:30:53.632] [jointLog] [info] iteration = 400 | max rel diff. = 0.415419
[2023-10-02 21:31:25.960] [jointLog] [info] iteration = 500 | max rel diff. = 0.0775898
[2023-10-02 21:31:58.310] [jointLog] [info] iteration = 600 | max rel diff. = 0.170389
[2023-10-02 21:32:30.277] [jointLog] [info] iteration = 700 | max rel diff. = 0.896873
[2023-10-02 21:33:02.064] [jointLog] [info] iteration = 800 | max rel diff. = 0.212113
[2023-10-02 21:33:34.160] [jointLog] [info] iteration = 900 | max rel diff. = 0.0236092
[2023-10-02 21:34:06.657] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.742381
[2023-10-02 21:34:07.291] [jointLog] [info] iteration = 1,003 | max rel diff. = 0.00405811
[2023-10-02 21:34:09.044] [jointLog] [info] Finished optimizer
[2023-10-02 21:34:09.044] [jointLog] [info] writing output