[2023-10-02 21:54:32.709] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 21:54:32.709] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 21:54:32.709] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 21:54:32.709] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 21:54:32.709] [jointLog] [info] parsing read library format
[2023-10-02 21:54:32.709] [jointLog] [info] There is 1 library.
[2023-10-02 21:54:32.710] [jointLog] [info] Loading pufferfish index
[2023-10-02 21:54:32.710] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 21:55:51.749] [jointLog] [info] done
[2023-10-02 21:55:51.921] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 21:56:33.354] [jointLog] [info] Number of decoys : 194
[2023-10-02 21:56:33.354] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 21:56:35.261] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 21:56:36.364] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 21:57:19.700] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-02 21:57:19.733] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-02 21:57:19.768] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-02 21:57:19.892] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-10-02 21:57:19.978] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-02 21:57:20.014] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-10-02 21:57:20.139] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-02 21:57:20.154] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-02 21:57:20.389] [fileLog] [info] 
At end of round 0
==================
Observed 3211735 total fragments (3211735 in most recent round)

[2023-10-02 21:57:20.387] [jointLog] [info] Computed 88,944 rich equivalence classes for further processing
[2023-10-02 21:57:20.387] [jointLog] [info] Counted 2,487,995 total reads in the equivalence classes 
[2023-10-02 21:57:20.398] [jointLog] [info] Number of mappings discarded because of alignment score : 46,750,440
[2023-10-02 21:57:20.398] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 283,504
[2023-10-02 21:57:20.398] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,544
[2023-10-02 21:57:20.398] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 21:57:22.274] [jointLog] [warning] Only 2487995 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 21:57:22.274] [jointLog] [info] Mapping rate = 77.4658%

[2023-10-02 21:57:22.274] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 21:57:22.274] [jointLog] [info] Starting optimizer
[2023-10-02 21:57:27.956] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 21:57:28.292] [jointLog] [info] iteration = 0 | max rel diff. = 51.1908
[2023-10-02 21:57:31.612] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 21:58:23.975] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 21:58:23.976] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 21:58:28.669] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 21:58:33.193] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 21:58:37.981] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 21:58:43.134] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 21:58:47.660] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 21:58:52.504] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 21:58:57.015] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 21:59:02.118] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 21:59:06.517] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 21:59:11.460] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 21:59:40.725] [jointLog] [info] iteration = 100 | max rel diff. = 19.9065
[2023-10-02 22:00:13.199] [jointLog] [info] iteration = 200 | max rel diff. = 0.81008
[2023-10-02 22:00:45.658] [jointLog] [info] iteration = 300 | max rel diff. = 0.170351
[2023-10-02 22:01:18.189] [jointLog] [info] iteration = 400 | max rel diff. = 10.5098
[2023-10-02 22:01:50.811] [jointLog] [info] iteration = 500 | max rel diff. = 0.188694
[2023-10-02 22:02:00.020] [jointLog] [info] iteration = 529 | max rel diff. = 0.00485169
[2023-10-02 22:02:01.879] [jointLog] [info] Finished optimizer
[2023-10-02 22:02:01.879] [jointLog] [info] writing output