[2023-09-01 18:59:29.370] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-01 18:59:29.370] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-01 18:59:29.370] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-01 18:59:29.370] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-01 18:59:29.370] [jointLog] [info] parsing read library format
[2023-09-01 18:59:29.370] [jointLog] [info] There is 1 library.
[2023-09-01 18:59:29.371] [jointLog] [info] Loading pufferfish index
[2023-09-01 18:59:29.371] [jointLog] [info] Loading dense pufferfish index.
[2023-09-01 19:00:47.151] [jointLog] [info] done
[2023-09-01 19:00:47.275] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-01 19:01:26.223] [jointLog] [info] Number of decoys : 194
[2023-09-01 19:01:26.223] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-01 19:01:27.828] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-01 19:01:28.469] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-01 19:02:45.451] [jointLog] [info] Thread saw mini-batch with a maximum of 1.82% zero probability fragments
[2023-09-01 19:02:45.484] [jointLog] [info] Thread saw mini-batch with a maximum of 1.74% zero probability fragments
[2023-09-01 19:02:45.492] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments
[2023-09-01 19:02:45.624] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments
[2023-09-01 19:02:45.625] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments
[2023-09-01 19:02:45.629] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments
[2023-09-01 19:02:45.681] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments
[2023-09-01 19:02:45.730] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments
[2023-09-01 19:02:45.959] [jointLog] [info] Computed 158,008 rich equivalence classes for further processing
[2023-09-01 19:02:45.959] [jointLog] [info] Counted 11,071,004 total reads in the equivalence classes 
[2023-09-01 19:02:45.969] [jointLog] [info] Number of mappings discarded because of alignment score : 11,761,462
[2023-09-01 19:02:45.969] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 353,535
[2023-09-01 19:02:45.969] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 109,090
[2023-09-01 19:02:45.969] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-01 19:02:45.969] [jointLog] [info] Mapping rate = 94.7928%

[2023-09-01 19:02:45.969] [jointLog] [info] finished quantifyLibrary()
[2023-09-01 19:02:45.970] [jointLog] [info] Starting optimizer
[2023-09-01 19:02:45.960] [fileLog] [info] 
At end of round 0
==================
Observed 11679157 total fragments (11679157 in most recent round)

[2023-09-01 19:02:57.310] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-01 19:02:57.637] [jointLog] [info] iteration = 0 | max rel diff. = 232.053
[2023-09-01 19:03:01.014] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-01 19:03:49.098] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-01 19:03:49.099] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-01 19:03:53.344] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-01 19:03:57.637] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-01 19:04:02.201] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-01 19:04:06.681] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-01 19:04:11.119] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-01 19:04:15.557] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-01 19:04:19.932] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-01 19:04:24.438] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-01 19:04:28.674] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-01 19:04:33.206] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-01 19:05:03.693] [jointLog] [info] iteration = 100 | max rel diff. = 14.1119
[2023-09-01 19:05:37.128] [jointLog] [info] iteration = 200 | max rel diff. = 5.21899
[2023-09-01 19:06:10.502] [jointLog] [info] iteration = 300 | max rel diff. = 20.6842
[2023-09-01 19:06:44.443] [jointLog] [info] iteration = 400 | max rel diff. = 2.444
[2023-09-01 19:07:17.921] [jointLog] [info] iteration = 500 | max rel diff. = 12.6188
[2023-09-01 19:07:51.089] [jointLog] [info] iteration = 600 | max rel diff. = 0.714591
[2023-09-01 19:08:24.517] [jointLog] [info] iteration = 700 | max rel diff. = 17.0081
[2023-09-01 19:08:57.845] [jointLog] [info] iteration = 800 | max rel diff. = 0.41729
[2023-09-01 19:09:30.943] [jointLog] [info] iteration = 900 | max rel diff. = 0.930542
[2023-09-01 19:10:04.633] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.863278
[2023-09-01 19:10:37.945] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0311545
[2023-09-01 19:10:59.397] [jointLog] [info] iteration = 1,166 | max rel diff. = 0.00654489
[2023-09-01 19:11:01.660] [jointLog] [info] Finished optimizer
[2023-09-01 19:11:01.660] [jointLog] [info] writing output