[2023-09-06 18:11:25.805] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-06 18:11:25.805] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-06 18:11:25.805] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-06 18:11:25.805] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-06 18:11:25.805] [jointLog] [info] parsing read library format
[2023-09-06 18:11:25.805] [jointLog] [info] There is 1 library.
[2023-09-06 18:11:25.805] [jointLog] [info] Loading pufferfish index
[2023-09-06 18:11:25.805] [jointLog] [info] Loading dense pufferfish index.
[2023-09-06 18:12:37.590] [jointLog] [info] done
[2023-09-06 18:12:37.709] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-06 18:13:13.145] [jointLog] [info] Number of decoys : 194
[2023-09-06 18:13:13.145] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-06 18:13:14.238] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-06 18:13:16.207] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-06 18:16:23.982] [jointLog] [info] Thread saw mini-batch with a maximum of 8.68% zero probability fragments
[2023-09-06 18:16:24.117] [jointLog] [info] Thread saw mini-batch with a maximum of 8.44% zero probability fragments
[2023-09-06 18:16:24.374] [jointLog] [info] Thread saw mini-batch with a maximum of 8.50% zero probability fragments
[2023-09-06 18:16:24.397] [jointLog] [info] Thread saw mini-batch with a maximum of 8.68% zero probability fragments
[2023-09-06 18:16:24.488] [jointLog] [info] Thread saw mini-batch with a maximum of 8.78% zero probability fragments
[2023-09-06 18:16:24.630] [jointLog] [info] Thread saw mini-batch with a maximum of 8.54% zero probability fragments
[2023-09-06 18:16:24.725] [jointLog] [info] Thread saw mini-batch with a maximum of 8.68% zero probability fragments
[2023-09-06 18:16:24.733] [jointLog] [info] Thread saw mini-batch with a maximum of 8.82% zero probability fragments
[2023-09-06 18:16:24.933] [jointLog] [info] Computed 167,309 rich equivalence classes for further processing
[2023-09-06 18:16:24.933] [jointLog] [info] Counted 5,455,968 total reads in the equivalence classes 
[2023-09-06 18:16:24.939] [jointLog] [info] Number of mappings discarded because of alignment score : 133,727,577
[2023-09-06 18:16:24.939] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,651,240
[2023-09-06 18:16:24.939] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 179,191
[2023-09-06 18:16:24.939] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-06 18:16:24.939] [jointLog] [info] Mapping rate = 66.1793%

[2023-09-06 18:16:24.939] [jointLog] [info] finished quantifyLibrary()
[2023-09-06 18:16:24.939] [jointLog] [info] Starting optimizer
[2023-09-06 18:16:24.934] [fileLog] [info] 
At end of round 0
==================
Observed 8244227 total fragments (8244227 in most recent round)

[2023-09-06 18:16:29.072] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-06 18:16:29.401] [jointLog] [info] iteration = 0 | max rel diff. = 108.178
[2023-09-06 18:16:32.726] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-06 18:17:43.399] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-06 18:17:43.400] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-06 18:17:49.810] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-06 18:17:56.030] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-06 18:18:02.553] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-06 18:18:09.037] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-06 18:18:15.541] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-06 18:18:22.057] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-06 18:18:28.491] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-06 18:18:34.724] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-06 18:18:41.419] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-06 18:18:47.796] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-06 18:18:47.831] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-06 18:19:20.685] [jointLog] [info] iteration = 100 | max rel diff. = 9.82818
[2023-09-06 18:19:54.486] [jointLog] [info] iteration = 200 | max rel diff. = 3.56443
[2023-09-06 18:20:27.933] [jointLog] [info] iteration = 300 | max rel diff. = 0.852777
[2023-09-06 18:21:01.663] [jointLog] [info] iteration = 400 | max rel diff. = 0.11816
[2023-09-06 18:21:34.723] [jointLog] [info] iteration = 500 | max rel diff. = 1.95001
[2023-09-06 18:22:07.191] [jointLog] [info] iteration = 600 | max rel diff. = 2.01154
[2023-09-06 18:22:40.027] [jointLog] [info] iteration = 700 | max rel diff. = 0.511638
[2023-09-06 18:23:12.874] [jointLog] [info] iteration = 800 | max rel diff. = 0.0186173
[2023-09-06 18:23:33.007] [jointLog] [info] iteration = 863 | max rel diff. = 0.00740057
[2023-09-06 18:23:35.081] [jointLog] [info] Finished optimizer
[2023-09-06 18:23:35.081] [jointLog] [info] writing output