[2023-09-20 15:42:50.191] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 15:42:50.191] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 15:42:50.191] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 15:42:50.191] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 15:42:50.191] [jointLog] [info] parsing read library format
[2023-09-20 15:42:50.191] [jointLog] [info] There is 1 library.
[2023-09-20 15:42:50.191] [jointLog] [info] Loading pufferfish index
[2023-09-20 15:42:50.192] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 15:44:03.219] [jointLog] [info] done
[2023-09-20 15:44:03.338] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 15:44:39.425] [jointLog] [info] Number of decoys : 194
[2023-09-20 15:44:39.425] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 15:44:41.017] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 15:44:42.179] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 15:45:15.084] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-20 15:45:15.162] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-20 15:45:15.236] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-20 15:45:15.264] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-20 15:45:15.284] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-20 15:45:15.293] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-20 15:45:15.326] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-09-20 15:45:15.819] [fileLog] [info] 
At end of round 0
==================
Observed 2167499 total fragments (2167499 in most recent round)

[2023-09-20 15:45:15.667] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-20 15:45:15.819] [jointLog] [info] Computed 73,346 rich equivalence classes for further processing
[2023-09-20 15:45:15.819] [jointLog] [info] Counted 1,692,173 total reads in the equivalence classes 
[2023-09-20 15:45:15.826] [jointLog] [info] Number of mappings discarded because of alignment score : 45,788,765
[2023-09-20 15:45:15.826] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 203,076
[2023-09-20 15:45:15.826] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 48,400
[2023-09-20 15:45:15.826] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 15:45:16.661] [jointLog] [warning] Only 1692173 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 15:45:16.661] [jointLog] [info] Mapping rate = 78.0703%

[2023-09-20 15:45:16.661] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 15:45:16.661] [jointLog] [info] Starting optimizer
[2023-09-20 15:45:20.504] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 15:45:20.842] [jointLog] [info] iteration = 0 | max rel diff. = 32.3234
[2023-09-20 15:45:24.175] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 15:46:12.175] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 15:46:12.175] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 15:46:15.905] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 15:46:20.223] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 15:46:24.781] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 15:46:29.176] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 15:46:33.587] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 15:46:38.239] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 15:46:42.444] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 15:46:46.535] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 15:46:50.978] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 15:46:55.721] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 15:47:25.457] [jointLog] [info] iteration = 100 | max rel diff. = 19.3361
[2023-09-20 15:47:57.101] [jointLog] [info] iteration = 200 | max rel diff. = 0.88928
[2023-09-20 15:48:32.933] [jointLog] [info] iteration = 300 | max rel diff. = 0.0888169
[2023-09-20 15:49:08.989] [jointLog] [info] iteration = 400 | max rel diff. = 0.19711
[2023-09-20 15:49:45.406] [jointLog] [info] iteration = 500 | max rel diff. = 0.0266039
[2023-09-20 15:50:19.125] [jointLog] [info] iteration = 600 | max rel diff. = 0.125127
[2023-09-20 15:50:51.360] [jointLog] [info] iteration = 700 | max rel diff. = 0.167175
[2023-09-20 15:51:15.575] [jointLog] [info] iteration = 772 | max rel diff. = 0.00670919
[2023-09-20 15:51:17.777] [jointLog] [info] Finished optimizer
[2023-09-20 15:51:17.777] [jointLog] [info] writing output