[2023-10-03 01:06:20.314] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 01:06:20.314] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 01:06:20.314] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 01:06:20.314] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 01:06:20.314] [jointLog] [info] parsing read library format
[2023-10-03 01:06:20.314] [jointLog] [info] There is 1 library.
[2023-10-03 01:06:20.314] [jointLog] [info] Loading pufferfish index
[2023-10-03 01:06:20.314] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 01:07:35.453] [jointLog] [info] done
[2023-10-03 01:07:35.611] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 01:08:16.061] [jointLog] [info] Number of decoys : 194
[2023-10-03 01:08:16.061] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 01:08:17.759] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 01:08:18.558] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 01:08:33.758] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-03 01:08:33.855] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-03 01:08:33.889] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-03 01:08:33.921] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-03 01:08:33.943] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-10-03 01:08:34.026] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-03 01:08:34.075] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-03 01:08:34.092] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-03 01:08:34.319] [fileLog] [info] 
At end of round 0
==================
Observed 1322468 total fragments (1322468 in most recent round)

[2023-10-03 01:08:34.318] [jointLog] [info] Computed 66,111 rich equivalence classes for further processing
[2023-10-03 01:08:34.318] [jointLog] [info] Counted 1,014,489 total reads in the equivalence classes 
[2023-10-03 01:08:34.328] [jointLog] [warning] 0.000302465% 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.


[2023-10-03 01:08:34.329] [jointLog] [info] Number of mappings discarded because of alignment score : 11,761,325
[2023-10-03 01:08:34.329] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 72,723
[2023-10-03 01:08:34.329] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 28,267
[2023-10-03 01:08:34.329] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 01:08:35.779] [jointLog] [warning] Only 1014489 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 01:08:35.779] [jointLog] [info] Mapping rate = 76.7118%

[2023-10-03 01:08:35.779] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 01:08:35.780] [jointLog] [info] Starting optimizer
[2023-10-03 01:08:39.457] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 01:08:39.776] [jointLog] [info] iteration = 0 | max rel diff. = 20.9986
[2023-10-03 01:08:43.044] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 01:09:25.991] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 01:09:25.991] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 01:09:29.799] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 01:09:33.619] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 01:09:37.461] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 01:09:41.770] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 01:09:45.832] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 01:09:49.957] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 01:09:54.017] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 01:09:58.202] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 01:10:02.154] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 01:10:05.964] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 01:10:38.015] [jointLog] [info] iteration = 100 | max rel diff. = 4.1771
[2023-10-03 01:11:11.924] [jointLog] [info] iteration = 200 | max rel diff. = 0.177733
[2023-10-03 01:11:46.718] [jointLog] [info] iteration = 300 | max rel diff. = 0.110193
[2023-10-03 01:12:20.496] [jointLog] [info] iteration = 400 | max rel diff. = 1.50145
[2023-10-03 01:12:53.433] [jointLog] [info] iteration = 500 | max rel diff. = 0.394782
[2023-10-03 01:13:26.393] [jointLog] [info] iteration = 600 | max rel diff. = 0.0428954
[2023-10-03 01:13:47.730] [jointLog] [info] iteration = 667 | max rel diff. = 0.00655642
[2023-10-03 01:13:50.468] [jointLog] [info] Finished optimizer
[2023-10-03 01:13:50.468] [jointLog] [info] writing output