[2023-10-04 16:03:20.435] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 16:03:20.435] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 16:03:20.435] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 16:03:20.435] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 16:03:20.435] [jointLog] [info] parsing read library format
[2023-10-04 16:03:20.435] [jointLog] [info] There is 1 library.
[2023-10-04 16:03:20.435] [jointLog] [info] Loading pufferfish index
[2023-10-04 16:03:20.435] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 16:04:49.627] [jointLog] [info] done
[2023-10-04 16:04:49.757] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 16:05:28.026] [jointLog] [info] Number of decoys : 194
[2023-10-04 16:05:28.026] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 16:05:29.523] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 16:05:30.124] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 16:06:17.432] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 16:06:17.585] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 16:06:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-10-04 16:06:17.603] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-04 16:06:17.715] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-10-04 16:06:17.771] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 16:06:17.836] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-04 16:06:17.891] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-10-04 16:06:18.041] [jointLog] [info] Computed 76,262 rich equivalence classes for further processing
[2023-10-04 16:06:18.041] [jointLog] [info] Counted 2,750,233 total reads in the equivalence classes 
[2023-10-04 16:06:18.047] [jointLog] [info] Number of mappings discarded because of alignment score : 49,693,711
[2023-10-04 16:06:18.047] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 271,857
[2023-10-04 16:06:18.047] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 80,977
[2023-10-04 16:06:18.047] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 16:06:18.042] [fileLog] [info] 
At end of round 0
==================
Observed 3570393 total fragments (3570393 in most recent round)

[2023-10-04 16:06:19.108] [jointLog] [warning] Only 2750233 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 16:06:19.108] [jointLog] [info] Mapping rate = 77.0289%

[2023-10-04 16:06:19.108] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 16:06:19.108] [jointLog] [info] Starting optimizer
[2023-10-04 16:06:22.703] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 16:06:23.033] [jointLog] [info] iteration = 0 | max rel diff. = 124.798
[2023-10-04 16:06:26.256] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 16:07:26.373] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 16:07:26.374] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 16:07:32.304] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 16:07:38.175] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 16:07:43.239] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 16:07:48.748] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 16:07:53.926] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 16:07:59.740] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 16:08:05.956] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 16:08:11.895] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 16:08:17.247] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 16:08:24.073] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 16:08:56.614] [jointLog] [info] iteration = 100 | max rel diff. = 11.9099
[2023-10-04 16:09:32.452] [jointLog] [info] iteration = 200 | max rel diff. = 13.5055
[2023-10-04 16:10:07.752] [jointLog] [info] iteration = 300 | max rel diff. = 0.239633
[2023-10-04 16:10:41.720] [jointLog] [info] iteration = 400 | max rel diff. = 0.0394147
[2023-10-04 16:11:18.559] [jointLog] [info] iteration = 500 | max rel diff. = 0.520594
[2023-10-04 16:11:53.997] [jointLog] [info] iteration = 600 | max rel diff. = 0.169301
[2023-10-04 16:12:27.893] [jointLog] [info] iteration = 700 | max rel diff. = 0.193064
[2023-10-04 16:12:54.847] [jointLog] [info] iteration = 776 | max rel diff. = 0.00584126
[2023-10-04 16:12:57.081] [jointLog] [info] Finished optimizer
[2023-10-04 16:12:57.081] [jointLog] [info] writing output