[2023-10-04 15:51:15.237] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 15:51:15.237] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 15:51:15.237] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 15:51:15.237] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 15:51:15.237] [jointLog] [info] parsing read library format
[2023-10-04 15:51:15.237] [jointLog] [info] There is 1 library.
[2023-10-04 15:51:15.237] [jointLog] [info] Loading pufferfish index
[2023-10-04 15:51:15.237] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 15:52:37.593] [jointLog] [info] done
[2023-10-04 15:52:37.732] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 15:53:16.347] [jointLog] [info] Number of decoys : 194
[2023-10-04 15:53:16.347] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 15:53:18.407] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 15:53:19.548] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 15:54:18.834] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-04 15:54:18.884] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-04 15:54:18.893] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-10-04 15:54:18.956] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-04 15:54:19.086] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-04 15:54:19.098] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-10-04 15:54:19.164] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-04 15:54:19.360] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 15:54:19.503] [jointLog] [info] Computed 80,852 rich equivalence classes for further processing
[2023-10-04 15:54:19.503] [jointLog] [info] Counted 3,267,996 total reads in the equivalence classes 
[2023-10-04 15:54:19.510] [jointLog] [info] Number of mappings discarded because of alignment score : 62,488,511
[2023-10-04 15:54:19.510] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 350,738
[2023-10-04 15:54:19.510] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 106,774
[2023-10-04 15:54:19.510] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 15:54:19.504] [fileLog] [info] 
At end of round 0
==================
Observed 4255636 total fragments (4255636 in most recent round)

[2023-10-04 15:54:20.601] [jointLog] [warning] Only 3267996 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 15:54:20.601] [jointLog] [info] Mapping rate = 76.7922%

[2023-10-04 15:54:20.601] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 15:54:20.602] [jointLog] [info] Starting optimizer
[2023-10-04 15:54:24.575] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 15:54:24.917] [jointLog] [info] iteration = 0 | max rel diff. = 64.1404
[2023-10-04 15:54:28.467] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 15:55:24.197] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 15:55:24.197] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 15:55:29.185] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 15:55:33.956] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 15:55:39.321] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 15:55:45.049] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 15:55:49.869] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 15:55:55.175] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 15:56:00.304] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 15:56:05.148] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 15:56:10.236] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 15:56:15.513] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 15:56:15.545] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 15:56:47.208] [jointLog] [info] iteration = 100 | max rel diff. = 4.8968
[2023-10-04 15:57:23.643] [jointLog] [info] iteration = 200 | max rel diff. = 2.51569
[2023-10-04 15:58:00.986] [jointLog] [info] iteration = 300 | max rel diff. = 0.156107
[2023-10-04 15:58:38.958] [jointLog] [info] iteration = 400 | max rel diff. = 4.25519
[2023-10-04 15:59:19.066] [jointLog] [info] iteration = 500 | max rel diff. = 0.329628
[2023-10-04 15:59:59.036] [jointLog] [info] iteration = 600 | max rel diff. = 0.09242
[2023-10-04 16:00:40.767] [jointLog] [info] iteration = 700 | max rel diff. = 0.0144566
[2023-10-04 16:01:18.681] [jointLog] [info] iteration = 800 | max rel diff. = 0.0148051
[2023-10-04 16:01:55.313] [jointLog] [info] iteration = 900 | max rel diff. = 0.073919
[2023-10-04 16:02:00.937] [jointLog] [info] iteration = 916 | max rel diff. = 0.00864272
[2023-10-04 16:02:02.997] [jointLog] [info] Finished optimizer
[2023-10-04 16:02:02.997] [jointLog] [info] writing output