[2023-10-03 08:24:52.049] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 08:24:52.049] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 08:24:52.049] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 08:24:52.049] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 08:24:52.049] [jointLog] [info] parsing read library format
[2023-10-03 08:24:52.049] [jointLog] [info] There is 1 library.
[2023-10-03 08:24:52.049] [jointLog] [info] Loading pufferfish index
[2023-10-03 08:24:52.049] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 08:26:10.003] [jointLog] [info] done
[2023-10-03 08:26:10.157] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 08:26:50.005] [jointLog] [info] Number of decoys : 194
[2023-10-03 08:26:50.005] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 08:26:51.677] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 08:26:52.697] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 08:27:33.639] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-10-03 08:27:33.712] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-03 08:27:33.801] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 08:27:33.874] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-03 08:27:33.930] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-03 08:27:33.934] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-03 08:27:34.036] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 08:27:34.068] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-03 08:27:34.279] [jointLog] [info] Computed 96,115 rich equivalence classes for further processing
[2023-10-03 08:27:34.279] [jointLog] [info] Counted 2,206,594 total reads in the equivalence classes 
[2023-10-03 08:27:34.288] [jointLog] [info] Number of mappings discarded because of alignment score : 44,612,885
[2023-10-03 08:27:34.288] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 267,263
[2023-10-03 08:27:34.288] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 67,279
[2023-10-03 08:27:34.288] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 08:27:34.280] [fileLog] [info] 
At end of round 0
==================
Observed 2911388 total fragments (2911388 in most recent round)

[2023-10-03 08:27:35.265] [jointLog] [warning] Only 2206594 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 08:27:35.265] [jointLog] [info] Mapping rate = 75.7918%

[2023-10-03 08:27:35.265] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 08:27:35.265] [jointLog] [info] Starting optimizer
[2023-10-03 08:27:39.690] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 08:27:40.037] [jointLog] [info] iteration = 0 | max rel diff. = 48.1223
[2023-10-03 08:27:43.443] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 08:28:41.219] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 08:28:41.219] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 08:28:46.167] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 08:28:51.537] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 08:28:56.744] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 08:29:02.298] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 08:29:07.725] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 08:29:12.917] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 08:29:18.196] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 08:29:23.155] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 08:29:28.555] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 08:29:33.859] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 08:29:33.859] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 08:30:04.209] [jointLog] [info] iteration = 100 | max rel diff. = 2.74776
[2023-10-03 08:30:37.038] [jointLog] [info] iteration = 200 | max rel diff. = 4.55667
[2023-10-03 08:31:09.834] [jointLog] [info] iteration = 300 | max rel diff. = 0.950899
[2023-10-03 08:31:42.441] [jointLog] [info] iteration = 400 | max rel diff. = 0.236079
[2023-10-03 08:32:14.903] [jointLog] [info] iteration = 500 | max rel diff. = 0.103068
[2023-10-03 08:32:47.336] [jointLog] [info] iteration = 600 | max rel diff. = 1.97327
[2023-10-03 08:33:19.383] [jointLog] [info] iteration = 700 | max rel diff. = 0.0209966
[2023-10-03 08:33:51.851] [jointLog] [info] iteration = 800 | max rel diff. = 0.231626
[2023-10-03 08:33:56.397] [jointLog] [info] iteration = 815 | max rel diff. = 0.00366872
[2023-10-03 08:33:58.369] [jointLog] [info] Finished optimizer
[2023-10-03 08:33:58.369] [jointLog] [info] writing output