[2023-10-05 07:31:57.097] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 07:31:57.097] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 07:31:57.097] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 07:31:57.097] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 07:31:57.097] [jointLog] [info] parsing read library format
[2023-10-05 07:31:57.097] [jointLog] [info] There is 1 library.
[2023-10-05 07:31:57.097] [jointLog] [info] Loading pufferfish index
[2023-10-05 07:31:57.097] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 07:33:15.071] [jointLog] [info] done
[2023-10-05 07:33:15.215] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 07:33:53.265] [jointLog] [info] Number of decoys : 194
[2023-10-05 07:33:53.265] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 07:33:55.014] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 07:33:55.755] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 07:34:41.093] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-10-05 07:34:41.142] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-05 07:34:41.192] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-05 07:34:41.238] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-05 07:34:41.289] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-10-05 07:34:41.344] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-05 07:34:41.374] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-05 07:34:41.443] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-05 07:34:41.571] [jointLog] [info] Computed 85,311 rich equivalence classes for further processing
[2023-10-05 07:34:41.571] [jointLog] [info] Counted 2,676,728 total reads in the equivalence classes 
[2023-10-05 07:34:41.578] [jointLog] [info] Number of mappings discarded because of alignment score : 49,557,527
[2023-10-05 07:34:41.578] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 257,805
[2023-10-05 07:34:41.578] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 80,367
[2023-10-05 07:34:41.578] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 07:34:41.572] [fileLog] [info] 
At end of round 0
==================
Observed 3726619 total fragments (3726619 in most recent round)

[2023-10-05 07:34:42.631] [jointLog] [warning] Only 2676728 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 07:34:42.631] [jointLog] [info] Mapping rate = 71.8273%

[2023-10-05 07:34:42.631] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 07:34:42.632] [jointLog] [info] Starting optimizer
[2023-10-05 07:34:47.035] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 07:34:47.372] [jointLog] [info] iteration = 0 | max rel diff. = 57.8209
[2023-10-05 07:34:50.700] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 07:35:50.590] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 07:35:50.590] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 07:35:55.955] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 07:36:01.595] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 07:36:06.920] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 07:36:12.423] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 07:36:18.016] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 07:36:23.613] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 07:36:29.247] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 07:36:34.675] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 07:36:40.103] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 07:36:45.777] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 07:37:15.654] [jointLog] [info] iteration = 100 | max rel diff. = 13.8551
[2023-10-05 07:37:48.711] [jointLog] [info] iteration = 200 | max rel diff. = 1.49527
[2023-10-05 07:38:21.059] [jointLog] [info] iteration = 300 | max rel diff. = 0.0964304
[2023-10-05 07:38:53.454] [jointLog] [info] iteration = 400 | max rel diff. = 0.211272
[2023-10-05 07:39:25.768] [jointLog] [info] iteration = 500 | max rel diff. = 0.452801
[2023-10-05 07:39:58.087] [jointLog] [info] iteration = 600 | max rel diff. = 0.219748
[2023-10-05 07:40:30.450] [jointLog] [info] iteration = 700 | max rel diff. = 0.723163
[2023-10-05 07:40:31.430] [jointLog] [info] iteration = 704 | max rel diff. = 0.00871818
[2023-10-05 07:40:33.545] [jointLog] [info] Finished optimizer
[2023-10-05 07:40:33.545] [jointLog] [info] writing output