[2023-09-28 14:22:15.399] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-28 14:22:15.399] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-28 14:22:15.399] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-28 14:22:15.399] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-28 14:22:15.399] [jointLog] [info] parsing read library format
[2023-09-28 14:22:15.399] [jointLog] [info] There is 1 library.
[2023-09-28 14:22:15.399] [jointLog] [info] Loading pufferfish index
[2023-09-28 14:22:15.400] [jointLog] [info] Loading dense pufferfish index.
[2023-09-28 14:23:27.809] [jointLog] [info] done
[2023-09-28 14:23:27.934] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-28 14:24:04.253] [jointLog] [info] Number of decoys : 194
[2023-09-28 14:24:04.253] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-28 14:24:05.836] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-28 14:24:07.288] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-28 14:24:48.321] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-09-28 14:24:48.520] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
[2023-09-28 14:24:48.520] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-28 14:24:48.558] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-28 14:24:48.577] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-09-28 14:24:48.614] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-28 14:24:48.684] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-09-28 14:24:48.760] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-28 14:24:48.920] [jointLog] [info] Computed 102,541 rich equivalence classes for further processing
[2023-09-28 14:24:48.920] [jointLog] [info] Counted 2,052,147 total reads in the equivalence classes 
[2023-09-28 14:24:48.927] [jointLog] [warning] 0.00011082% 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.


[2023-09-28 14:24:48.927] [jointLog] [info] Number of mappings discarded because of alignment score : 45,650,449
[2023-09-28 14:24:48.927] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 215,830
[2023-09-28 14:24:48.927] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 64,384
[2023-09-28 14:24:48.927] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-28 14:24:48.921] [fileLog] [info] 
At end of round 0
==================
Observed 2707100 total fragments (2707100 in most recent round)

[2023-09-28 14:24:49.614] [jointLog] [warning] Only 2052147 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-28 14:24:49.614] [jointLog] [info] Mapping rate = 75.8061%

[2023-09-28 14:24:49.614] [jointLog] [info] finished quantifyLibrary()
[2023-09-28 14:24:49.614] [jointLog] [info] Starting optimizer
[2023-09-28 14:24:53.145] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-28 14:24:53.474] [jointLog] [info] iteration = 0 | max rel diff. = 43.4149
[2023-09-28 14:24:56.734] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-28 14:26:01.353] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-28 14:26:01.353] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-28 14:26:07.501] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-28 14:26:13.216] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-28 14:26:19.207] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-28 14:26:25.363] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-28 14:26:31.249] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-28 14:26:37.471] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-28 14:26:43.397] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-28 14:26:49.052] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-28 14:26:55.132] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-28 14:27:00.720] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-28 14:27:31.055] [jointLog] [info] iteration = 100 | max rel diff. = 3.76729
[2023-09-28 14:28:03.009] [jointLog] [info] iteration = 200 | max rel diff. = 1.28267
[2023-09-28 14:28:34.252] [jointLog] [info] iteration = 300 | max rel diff. = 0.103037
[2023-09-28 14:29:05.550] [jointLog] [info] iteration = 400 | max rel diff. = 0.206909
[2023-09-28 14:29:38.138] [jointLog] [info] iteration = 500 | max rel diff. = 0.226296
[2023-09-28 14:30:10.306] [jointLog] [info] iteration = 600 | max rel diff. = 1.75003
[2023-09-28 14:30:42.081] [jointLog] [info] iteration = 700 | max rel diff. = 0.0350186
[2023-09-28 14:31:14.399] [jointLog] [info] iteration = 800 | max rel diff. = 0.0157441
[2023-09-28 14:31:46.162] [jointLog] [info] iteration = 900 | max rel diff. = 0.0363138
[2023-09-28 14:31:55.702] [jointLog] [info] iteration = 931 | max rel diff. = 0.000621216
[2023-09-28 14:31:57.499] [jointLog] [info] Finished optimizer
[2023-09-28 14:31:57.499] [jointLog] [info] writing output