[2023-09-29 09:32:56.173] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-29 09:32:56.173] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-29 09:32:56.173] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-29 09:32:56.173] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-29 09:32:56.173] [jointLog] [info] parsing read library format
[2023-09-29 09:32:56.174] [jointLog] [info] There is 1 library.
[2023-09-29 09:32:56.174] [jointLog] [info] Loading pufferfish index
[2023-09-29 09:32:56.174] [jointLog] [info] Loading dense pufferfish index.
[2023-09-29 09:34:10.336] [jointLog] [info] done
[2023-09-29 09:34:10.475] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-29 09:34:44.726] [jointLog] [info] Number of decoys : 194
[2023-09-29 09:34:44.726] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-29 09:34:46.227] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-29 09:34:47.150] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-29 09:35:01.420] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-09-29 09:35:01.442] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-29 09:35:01.491] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-09-29 09:35:01.527] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-29 09:35:01.710] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-09-29 09:35:01.807] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-09-29 09:35:01.883] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-09-29 09:35:01.884] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-09-29 09:35:02.043] [jointLog] [info] Computed 62,332 rich equivalence classes for further processing
[2023-09-29 09:35:02.043] [jointLog] [info] Counted 756,528 total reads in the equivalence classes 
[2023-09-29 09:35:02.050] [jointLog] [warning] 9.97166e-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 23.


[2023-09-29 09:35:02.050] [jointLog] [info] Number of mappings discarded because of alignment score : 15,230,385
[2023-09-29 09:35:02.050] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 83,889
[2023-09-29 09:35:02.050] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 26,391
[2023-09-29 09:35:02.050] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-29 09:35:02.044] [fileLog] [info] 
At end of round 0
==================
Observed 1002842 total fragments (1002842 in most recent round)

[2023-09-29 09:35:02.939] [jointLog] [warning] Only 756528 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-29 09:35:02.939] [jointLog] [info] Mapping rate = 75.4384%

[2023-09-29 09:35:02.939] [jointLog] [info] finished quantifyLibrary()
[2023-09-29 09:35:02.940] [jointLog] [info] Starting optimizer
[2023-09-29 09:35:06.421] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-29 09:35:06.738] [jointLog] [info] iteration = 0 | max rel diff. = 14.1516
[2023-09-29 09:35:09.960] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-29 09:35:59.423] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-29 09:35:59.424] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-29 09:36:04.180] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-29 09:36:08.604] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-29 09:36:12.952] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-29 09:36:17.423] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-29 09:36:21.798] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-29 09:36:26.198] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-29 09:36:30.775] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-29 09:36:34.983] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-29 09:36:39.628] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-29 09:36:43.800] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-29 09:37:14.775] [jointLog] [info] iteration = 100 | max rel diff. = 16.6203
[2023-09-29 09:37:48.557] [jointLog] [info] iteration = 200 | max rel diff. = 0.224917
[2023-09-29 09:38:22.339] [jointLog] [info] iteration = 300 | max rel diff. = 0.0435772
[2023-09-29 09:38:56.108] [jointLog] [info] iteration = 400 | max rel diff. = 0.125598
[2023-09-29 09:39:01.149] [jointLog] [info] iteration = 416 | max rel diff. = 0.00952761
[2023-09-29 09:39:03.198] [jointLog] [info] Finished optimizer
[2023-09-29 09:39:03.198] [jointLog] [info] writing output