[2023-09-28 08:16:43.537] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-28 08:16:43.537] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-28 08:16:43.537] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-28 08:16:43.537] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-28 08:16:43.537] [jointLog] [info] parsing read library format
[2023-09-28 08:16:43.537] [jointLog] [info] There is 1 library.
[2023-09-28 08:16:43.538] [jointLog] [info] Loading pufferfish index
[2023-09-28 08:16:43.538] [jointLog] [info] Loading dense pufferfish index.
[2023-09-28 08:17:59.732] [jointLog] [info] done
[2023-09-28 08:17:59.859] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-28 08:18:34.992] [jointLog] [info] Number of decoys : 194
[2023-09-28 08:18:34.992] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-28 08:18:37.035] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-28 08:18:37.919] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-28 08:19:18.416] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-28 08:19:18.523] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-28 08:19:18.595] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-09-28 08:19:18.642] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-28 08:19:18.757] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-28 08:19:18.773] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-09-28 08:19:18.841] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-28 08:19:18.847] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-28 08:19:19.018] [jointLog] [info] Computed 101,596 rich equivalence classes for further processing
[2023-09-28 08:19:19.018] [jointLog] [info] Counted 2,512,179 total reads in the equivalence classes 
[2023-09-28 08:19:19.026] [jointLog] [warning] 0.000123443% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 10.


[2023-09-28 08:19:19.026] [jointLog] [info] Number of mappings discarded because of alignment score : 43,642,726
[2023-09-28 08:19:19.026] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 241,513
[2023-09-28 08:19:19.026] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 69,260
[2023-09-28 08:19:19.026] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-28 08:19:19.019] [fileLog] [info] 
At end of round 0
==================
Observed 3240368 total fragments (3240368 in most recent round)

[2023-09-28 08:19:19.821] [jointLog] [warning] Only 2512179 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-28 08:19:19.821] [jointLog] [info] Mapping rate = 77.5276%

[2023-09-28 08:19:19.821] [jointLog] [info] finished quantifyLibrary()
[2023-09-28 08:19:19.822] [jointLog] [info] Starting optimizer
[2023-09-28 08:19:23.394] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-28 08:19:23.747] [jointLog] [info] iteration = 0 | max rel diff. = 57.2152
[2023-09-28 08:19:27.255] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-28 08:20:31.924] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-28 08:20:31.924] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-28 08:20:37.870] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-28 08:20:43.803] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-28 08:20:50.154] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-28 08:20:56.406] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-28 08:21:02.404] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-28 08:21:08.443] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-28 08:21:13.945] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-28 08:21:19.718] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-28 08:21:25.903] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-28 08:21:32.008] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 08:22:03.678] [jointLog] [info] iteration = 100 | max rel diff. = 5.14792
[2023-09-28 08:22:40.731] [jointLog] [info] iteration = 200 | max rel diff. = 1.0833
[2023-09-28 08:23:15.313] [jointLog] [info] iteration = 300 | max rel diff. = 0.53211
[2023-09-28 08:23:49.758] [jointLog] [info] iteration = 400 | max rel diff. = 1.10699
[2023-09-28 08:24:24.194] [jointLog] [info] iteration = 500 | max rel diff. = 3.26526
[2023-09-28 08:24:33.030] [jointLog] [info] iteration = 528 | max rel diff. = 0.0060716
[2023-09-28 08:24:34.840] [jointLog] [info] Finished optimizer
[2023-09-28 08:24:34.840] [jointLog] [info] writing output