[2022-06-14 19:01:28.193] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-06-14 19:01:28.193] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-06-14 19:01:28.193] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-06-14 19:01:28.193] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-06-14 19:01:28.193] [jointLog] [info] parsing read library format
[2022-06-14 19:01:28.193] [jointLog] [info] There is 1 library.
[2022-06-14 19:01:28.193] [jointLog] [info] Loading pufferfish index
[2022-06-14 19:01:28.193] [jointLog] [info] Loading dense pufferfish index.
[2022-06-14 19:04:17.557] [jointLog] [info] done
[2022-06-14 19:04:17.798] [jointLog] [info] Index contained 5,382,683 targets
[2022-06-14 19:05:36.427] [jointLog] [info] Number of decoys : 194
[2022-06-14 19:05:36.427] [jointLog] [info] First decoy index : 5,185,409 
[2022-06-14 19:05:39.878] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2022-06-14 19:05:42.323] [jointLog] [info] Automatically detected most likely library type as SF

[2022-06-14 19:12:58.799] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments
[2022-06-14 19:12:58.863] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments
[2022-06-14 19:12:58.907] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments
[2022-06-14 19:12:59.396] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments
[2022-06-14 19:12:59.458] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments
[2022-06-14 19:12:59.536] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments
[2022-06-14 19:12:59.977] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments
[2022-06-14 19:13:00.120] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments
[2022-06-14 19:13:00.682] [fileLog] [info] 
At end of round 0
==================
Observed 11619954 total fragments (11619954 in most recent round)

[2022-06-14 19:13:00.674] [jointLog] [info] Computed 134,609 rich equivalence classes for further processing
[2022-06-14 19:13:00.674] [jointLog] [info] Counted 7,201,444 total reads in the equivalence classes 
[2022-06-14 19:13:00.699] [jointLog] [info] Number of mappings discarded because of alignment score : 104,247,421
[2022-06-14 19:13:00.699] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,902,895
[2022-06-14 19:13:00.699] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 345,856
[2022-06-14 19:13:00.699] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2022-06-14 19:13:00.699] [jointLog] [info] Mapping rate = 61.9748%

[2022-06-14 19:13:00.699] [jointLog] [info] finished quantifyLibrary()
[2022-06-14 19:13:00.700] [jointLog] [info] Starting optimizer
[2022-06-14 19:13:08.482] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-06-14 19:13:09.349] [jointLog] [info] iteration = 0 | max rel diff. = 128.456
[2022-06-14 19:13:17.123] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-06-14 19:16:26.728] [jointLog] [info] Computed expected counts (for bias correction)
[2022-06-14 19:16:26.729] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-06-14 19:16:46.979] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-06-14 19:17:09.380] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-06-14 19:17:31.785] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-06-14 19:17:54.079] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-06-14 19:18:15.173] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-06-14 19:18:35.492] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-06-14 19:18:56.555] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-06-14 19:19:16.926] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-06-14 19:19:37.905] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-06-14 19:19:59.403] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-06-14 19:19:59.468] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-06-14 19:21:05.628] [jointLog] [info] iteration = 100 | max rel diff. = 13.1848
[2022-06-14 19:22:21.945] [jointLog] [info] iteration = 200 | max rel diff. = 6.80211
[2022-06-14 19:23:44.298] [jointLog] [info] iteration = 300 | max rel diff. = 0.650868
[2022-06-14 19:25:06.024] [jointLog] [info] iteration = 400 | max rel diff. = 1.63665
[2022-06-14 19:26:24.544] [jointLog] [info] iteration = 500 | max rel diff. = 0.0316145
[2022-06-14 19:27:48.378] [jointLog] [info] iteration = 600 | max rel diff. = 0.180289
[2022-06-14 19:29:05.856] [jointLog] [info] iteration = 700 | max rel diff. = 0.0192315
[2022-06-14 19:30:26.022] [jointLog] [info] iteration = 800 | max rel diff. = 0.251459
[2022-06-14 19:31:51.557] [jointLog] [info] iteration = 900 | max rel diff. = 0.138372
[2022-06-14 19:32:59.408] [jointLog] [info] iteration = 982 | max rel diff. = 0.0058627
[2022-06-14 19:33:03.286] [jointLog] [info] Finished optimizer
[2022-06-14 19:33:03.291] [jointLog] [info] writing output