[2023-09-26 05:24:10.883] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-26 05:24:10.883] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-26 05:24:10.883] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-26 05:24:10.883] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-26 05:24:10.883] [jointLog] [info] parsing read library format
[2023-09-26 05:24:10.883] [jointLog] [info] There is 1 library.
[2023-09-26 05:24:10.883] [jointLog] [info] Loading pufferfish index
[2023-09-26 05:24:10.883] [jointLog] [info] Loading dense pufferfish index.
[2023-09-26 05:25:33.432] [jointLog] [info] done
[2023-09-26 05:25:33.585] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-26 05:26:13.161] [jointLog] [info] Number of decoys : 194
[2023-09-26 05:26:13.161] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-26 05:26:15.209] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-26 05:26:16.099] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-26 05:27:06.191] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-26 05:27:06.352] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-09-26 05:27:06.394] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-26 05:27:06.433] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-26 05:27:06.440] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-26 05:27:06.537] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-26 05:27:06.614] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-26 05:27:06.649] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-26 05:27:06.829] [jointLog] [info] Computed 86,606 rich equivalence classes for further processing
[2023-09-26 05:27:06.829] [jointLog] [info] Counted 2,147,556 total reads in the equivalence classes 
[2023-09-26 05:27:06.837] [jointLog] [warning] 6.7697e-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.


[2023-09-26 05:27:06.837] [jointLog] [info] Number of mappings discarded because of alignment score : 75,323,280
[2023-09-26 05:27:06.837] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 333,356
[2023-09-26 05:27:06.837] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 83,779
[2023-09-26 05:27:06.837] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-26 05:27:06.830] [fileLog] [info] 
At end of round 0
==================
Observed 2954339 total fragments (2954339 in most recent round)

[2023-09-26 05:27:07.817] [jointLog] [warning] Only 2147556 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-26 05:27:07.817] [jointLog] [info] Mapping rate = 72.6916%

[2023-09-26 05:27:07.817] [jointLog] [info] finished quantifyLibrary()
[2023-09-26 05:27:07.817] [jointLog] [info] Starting optimizer
[2023-09-26 05:27:11.412] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-26 05:27:11.739] [jointLog] [info] iteration = 0 | max rel diff. = 40.011
[2023-09-26 05:27:15.031] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-26 05:28:09.112] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-26 05:28:09.112] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-26 05:28:13.785] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-26 05:28:18.233] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-26 05:28:23.458] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-26 05:28:28.356] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-26 05:28:33.244] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-26 05:28:38.596] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-26 05:28:43.462] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-26 05:28:48.224] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-26 05:28:52.973] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-26 05:28:58.248] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-26 05:29:26.453] [jointLog] [info] iteration = 100 | max rel diff. = 3.9954
[2023-09-26 05:29:58.317] [jointLog] [info] iteration = 200 | max rel diff. = 0.83288
[2023-09-26 05:30:30.134] [jointLog] [info] iteration = 300 | max rel diff. = 0.377131
[2023-09-26 05:31:02.926] [jointLog] [info] iteration = 400 | max rel diff. = 0.585671
[2023-09-26 05:31:35.579] [jointLog] [info] iteration = 500 | max rel diff. = 0.0888923
[2023-09-26 05:31:46.411] [jointLog] [info] iteration = 534 | max rel diff. = 0.0087382
[2023-09-26 05:31:48.187] [jointLog] [info] Finished optimizer
[2023-09-26 05:31:48.187] [jointLog] [info] writing output