[2023-10-03 09:16:29.451] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 09:16:29.451] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 09:16:29.451] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 09:16:29.451] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 09:16:29.451] [jointLog] [info] parsing read library format
[2023-10-03 09:16:29.451] [jointLog] [info] There is 1 library.
[2023-10-03 09:16:29.451] [jointLog] [info] Loading pufferfish index
[2023-10-03 09:16:29.451] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 09:17:46.829] [jointLog] [info] done
[2023-10-03 09:17:46.993] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 09:18:28.595] [jointLog] [info] Number of decoys : 194
[2023-10-03 09:18:28.595] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 09:18:30.742] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 09:18:31.976] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 09:19:18.174] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-03 09:19:18.310] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-03 09:19:18.430] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 09:19:18.448] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 09:19:18.517] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 09:19:18.652] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-10-03 09:19:18.666] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-03 09:19:18.670] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-03 09:19:18.870] [jointLog] [info] Computed 90,462 rich equivalence classes for further processing
[2023-10-03 09:19:18.870] [jointLog] [info] Counted 1,960,445 total reads in the equivalence classes 
[2023-10-03 09:19:18.879] [jointLog] [warning] 3.95974e-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 30.


[2023-10-03 09:19:18.879] [jointLog] [info] Number of mappings discarded because of alignment score : 41,457,946
[2023-10-03 09:19:18.879] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 234,955
[2023-10-03 09:19:18.879] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 51,634
[2023-10-03 09:19:18.879] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 09:19:18.871] [fileLog] [info] 
At end of round 0
==================
Observed 2525419 total fragments (2525419 in most recent round)

[2023-10-03 09:19:20.259] [jointLog] [warning] Only 1960445 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 09:19:20.259] [jointLog] [info] Mapping rate = 77.6285%

[2023-10-03 09:19:20.259] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 09:19:20.259] [jointLog] [info] Starting optimizer
[2023-10-03 09:19:25.262] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 09:19:25.601] [jointLog] [info] iteration = 0 | max rel diff. = 39.7703
[2023-10-03 09:19:28.950] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 09:20:24.853] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 09:20:24.853] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 09:20:29.764] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 09:20:34.543] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 09:20:39.507] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 09:20:44.727] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 09:20:49.756] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 09:20:55.246] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 09:21:00.043] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 09:21:05.120] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 09:21:10.092] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 09:21:15.186] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 09:21:45.633] [jointLog] [info] iteration = 100 | max rel diff. = 14.3352
[2023-10-03 09:22:19.923] [jointLog] [info] iteration = 200 | max rel diff. = 0.35327
[2023-10-03 09:22:54.590] [jointLog] [info] iteration = 300 | max rel diff. = 0.898535
[2023-10-03 09:23:28.995] [jointLog] [info] iteration = 400 | max rel diff. = 0.210592
[2023-10-03 09:24:03.700] [jointLog] [info] iteration = 500 | max rel diff. = 0.104614
[2023-10-03 09:24:37.978] [jointLog] [info] iteration = 600 | max rel diff. = 0.01095
[2023-10-03 09:25:12.408] [jointLog] [info] iteration = 700 | max rel diff. = 0.22725
[2023-10-03 09:25:46.768] [jointLog] [info] iteration = 800 | max rel diff. = 0.0256851
[2023-10-03 09:25:59.063] [jointLog] [info] iteration = 837 | max rel diff. = 0.00202911
[2023-10-03 09:26:01.203] [jointLog] [info] Finished optimizer
[2023-10-03 09:26:01.203] [jointLog] [info] writing output