[2023-09-20 06:03:27.338] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-20 06:03:27.338] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-20 06:03:27.338] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-20 06:03:27.338] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-20 06:03:27.338] [jointLog] [info] parsing read library format
[2023-09-20 06:03:27.338] [jointLog] [info] There is 1 library.
[2023-09-20 06:03:27.338] [jointLog] [info] Loading pufferfish index
[2023-09-20 06:03:27.338] [jointLog] [info] Loading dense pufferfish index.
[2023-09-20 06:04:43.308] [jointLog] [info] done
[2023-09-20 06:04:43.438] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-20 06:05:20.852] [jointLog] [info] Number of decoys : 194
[2023-09-20 06:05:20.852] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-20 06:05:22.874] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-20 06:05:23.839] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-20 06:05:48.134] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
[2023-09-20 06:05:48.223] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-09-20 06:05:48.275] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-20 06:05:48.297] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-09-20 06:05:48.338] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-20 06:05:48.341] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-20 06:05:48.351] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-20 06:05:48.355] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-09-20 06:05:48.543] [jointLog] [info] Computed 78,196 rich equivalence classes for further processing
[2023-09-20 06:05:48.543] [jointLog] [info] Counted 1,395,959 total reads in the equivalence classes 
[2023-09-20 06:05:48.544] [fileLog] [info] 
At end of round 0
==================
Observed 1834759 total fragments (1834759 in most recent round)

[2023-09-20 06:05:48.552] [jointLog] [warning] 0.000163509% 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.


[2023-09-20 06:05:48.552] [jointLog] [info] Number of mappings discarded because of alignment score : 25,012,612
[2023-09-20 06:05:48.552] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 148,412
[2023-09-20 06:05:48.552] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 47,044
[2023-09-20 06:05:48.552] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-20 06:05:50.051] [jointLog] [warning] Only 1395959 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-20 06:05:50.051] [jointLog] [info] Mapping rate = 76.0841%

[2023-09-20 06:05:50.051] [jointLog] [info] finished quantifyLibrary()
[2023-09-20 06:05:50.053] [jointLog] [info] Starting optimizer
[2023-09-20 06:05:55.962] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-20 06:05:56.327] [jointLog] [info] iteration = 0 | max rel diff. = 28.1884
[2023-09-20 06:05:59.985] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-20 06:06:57.478] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-20 06:06:57.479] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-20 06:07:02.451] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-20 06:07:07.794] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-20 06:07:13.035] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-20 06:07:18.190] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-20 06:07:23.311] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-20 06:07:28.563] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-20 06:07:33.727] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-20 06:07:39.138] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-20 06:07:44.321] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-20 06:07:49.332] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-20 06:08:21.806] [jointLog] [info] iteration = 100 | max rel diff. = 12.364
[2023-09-20 06:08:58.169] [jointLog] [info] iteration = 200 | max rel diff. = 0.772981
[2023-09-20 06:09:34.542] [jointLog] [info] iteration = 300 | max rel diff. = 5.76977
[2023-09-20 06:10:12.282] [jointLog] [info] iteration = 400 | max rel diff. = 0.0347377
[2023-09-20 06:10:49.746] [jointLog] [info] iteration = 500 | max rel diff. = 0.384265
[2023-09-20 06:11:27.395] [jointLog] [info] iteration = 600 | max rel diff. = 0.443161
[2023-09-20 06:11:52.376] [jointLog] [info] iteration = 668 | max rel diff. = 0.00666958
[2023-09-20 06:11:55.104] [jointLog] [info] Finished optimizer
[2023-09-20 06:11:55.104] [jointLog] [info] writing output