[2023-08-21 18:25:51.981] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-21 18:25:51.981] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-21 18:25:51.981] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-21 18:25:51.981] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-21 18:25:51.981] [jointLog] [info] parsing read library format
[2023-08-21 18:25:51.981] [jointLog] [info] There is 1 library.
[2023-08-21 18:25:51.981] [jointLog] [info] Loading pufferfish index
[2023-08-21 18:25:51.981] [jointLog] [info] Loading dense pufferfish index.
[2023-08-21 18:27:10.197] [jointLog] [info] done
[2023-08-21 18:27:10.324] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-21 18:27:50.852] [jointLog] [info] Number of decoys : 194
[2023-08-21 18:27:50.852] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-21 18:27:53.862] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-21 18:29:01.600] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-08-21 18:29:01.710] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-08-21 18:29:01.730] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-08-21 18:29:01.789] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-08-21 18:29:01.802] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-08-21 18:29:02.003] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-08-21 18:29:02.095] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
[2023-08-21 18:29:02.186] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-08-21 18:29:02.492] [fileLog] [info] 
At end of round 0
==================
Observed 3631879 total fragments (3631879 in most recent round)

[2023-08-21 18:29:02.492] [jointLog] [info] Computed 115,069 rich equivalence classes for further processing
[2023-08-21 18:29:02.492] [jointLog] [info] Counted 3,228,746 total reads in the equivalence classes 
[2023-08-21 18:29:02.498] [jointLog] [info] Number of mappings discarded because of alignment score : 1,535,059
[2023-08-21 18:29:02.498] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 247,583
[2023-08-21 18:29:02.498] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 113,774
[2023-08-21 18:29:02.498] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 395,559
[2023-08-21 18:29:04.036] [jointLog] [warning] Only 3228746 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-08-21 18:29:04.036] [jointLog] [info] Mapping rate = 88.9002%

[2023-08-21 18:29:04.036] [jointLog] [info] finished quantifyLibrary()
[2023-08-21 18:29:04.037] [jointLog] [info] Starting optimizer
[2023-08-21 18:29:10.733] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-21 18:29:11.359] [jointLog] [info] iteration = 0 | max rel diff. = 58.6272
[2023-08-21 18:29:16.790] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-21 18:33:27.021] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-21 18:33:27.021] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-21 18:33:47.678] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-21 18:34:08.021] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-21 18:34:29.292] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-21 18:34:51.965] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-21 18:35:12.839] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-21 18:35:34.041] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-21 18:35:55.714] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-21 18:36:18.181] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-21 18:36:38.940] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-21 18:37:00.096] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 18:37:00.215] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 18:37:44.496] [jointLog] [info] iteration = 100 | max rel diff. = 9.90676
[2023-08-21 18:38:29.054] [jointLog] [info] iteration = 200 | max rel diff. = 5.71884
[2023-08-21 18:39:08.976] [jointLog] [info] iteration = 300 | max rel diff. = 0.112516
[2023-08-21 18:39:55.293] [jointLog] [info] iteration = 400 | max rel diff. = 0.148032
[2023-08-21 18:40:42.603] [jointLog] [info] iteration = 500 | max rel diff. = 0.119636
[2023-08-21 18:41:24.119] [jointLog] [info] iteration = 600 | max rel diff. = 0.0353584
[2023-08-21 18:42:11.490] [jointLog] [info] iteration = 700 | max rel diff. = 0.320447
[2023-08-21 18:42:56.966] [jointLog] [info] iteration = 800 | max rel diff. = 0.0705928
[2023-08-21 18:43:41.568] [jointLog] [info] iteration = 900 | max rel diff. = 0.0329349
[2023-08-21 18:44:23.287] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0296321
[2023-08-21 18:44:37.937] [jointLog] [info] iteration = 1,034 | max rel diff. = 0.000565085
[2023-08-21 18:44:39.877] [jointLog] [info] Finished optimizer
[2023-08-21 18:44:39.877] [jointLog] [info] writing output