[2023-10-05 03:29:30.114] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 03:29:30.114] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 03:29:30.114] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 03:29:30.114] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 03:29:30.114] [jointLog] [info] parsing read library format
[2023-10-05 03:29:30.114] [jointLog] [info] There is 1 library.
[2023-10-05 03:29:30.114] [jointLog] [info] Loading pufferfish index
[2023-10-05 03:29:30.114] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 03:30:45.736] [jointLog] [info] done
[2023-10-05 03:30:45.867] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 03:31:23.838] [jointLog] [info] Number of decoys : 194
[2023-10-05 03:31:23.838] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 03:31:25.292] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 03:31:26.406] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 03:32:08.832] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
[2023-10-05 03:32:08.889] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-10-05 03:32:08.938] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-05 03:32:09.016] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-05 03:32:09.093] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-05 03:32:09.124] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-10-05 03:32:09.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-10-05 03:32:09.252] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-05 03:32:09.404] [jointLog] [info] Computed 81,797 rich equivalence classes for further processing
[2023-10-05 03:32:09.404] [jointLog] [info] Counted 2,352,118 total reads in the equivalence classes 
[2023-10-05 03:32:09.411] [jointLog] [warning] 3.21454e-05% 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.


[2023-10-05 03:32:09.411] [jointLog] [info] Number of mappings discarded because of alignment score : 51,639,878
[2023-10-05 03:32:09.411] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 269,920
[2023-10-05 03:32:09.411] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 85,837
[2023-10-05 03:32:09.411] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 03:32:09.405] [fileLog] [info] 
At end of round 0
==================
Observed 3110868 total fragments (3110868 in most recent round)

[2023-10-05 03:32:10.352] [jointLog] [warning] Only 2352118 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 03:32:10.352] [jointLog] [info] Mapping rate = 75.6097%

[2023-10-05 03:32:10.352] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 03:32:10.353] [jointLog] [info] Starting optimizer
[2023-10-05 03:32:14.326] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 03:32:14.641] [jointLog] [info] iteration = 0 | max rel diff. = 59.8853
[2023-10-05 03:32:17.766] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 03:33:08.050] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 03:33:08.050] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 03:33:12.451] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 03:33:16.846] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 03:33:21.558] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 03:33:26.354] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 03:33:30.945] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 03:33:35.834] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 03:33:40.376] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 03:33:45.032] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 03:33:49.594] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 03:33:54.082] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 03:34:22.600] [jointLog] [info] iteration = 100 | max rel diff. = 1.21315
[2023-10-05 03:34:54.371] [jointLog] [info] iteration = 200 | max rel diff. = 0.414609
[2023-10-05 03:35:26.398] [jointLog] [info] iteration = 300 | max rel diff. = 0.298441
[2023-10-05 03:35:57.647] [jointLog] [info] iteration = 400 | max rel diff. = 0.115854
[2023-10-05 03:36:29.908] [jointLog] [info] iteration = 500 | max rel diff. = 0.0729782
[2023-10-05 03:37:01.406] [jointLog] [info] iteration = 600 | max rel diff. = 0.998002
[2023-10-05 03:37:34.008] [jointLog] [info] iteration = 700 | max rel diff. = 0.234234
[2023-10-05 03:37:54.089] [jointLog] [info] iteration = 765 | max rel diff. = 0.0073881
[2023-10-05 03:37:56.067] [jointLog] [info] Finished optimizer
[2023-10-05 03:37:56.067] [jointLog] [info] writing output