[2023-09-16 07:24:29.129] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-16 07:24:29.129] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-16 07:24:29.129] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-16 07:24:29.129] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-16 07:24:29.129] [jointLog] [info] parsing read library format
[2023-09-16 07:24:29.129] [jointLog] [info] There is 1 library.
[2023-09-16 07:24:29.130] [jointLog] [info] Loading pufferfish index
[2023-09-16 07:24:29.130] [jointLog] [info] Loading dense pufferfish index.
[2023-09-16 07:25:48.645] [jointLog] [info] done
[2023-09-16 07:25:48.773] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-16 07:26:27.856] [jointLog] [info] Number of decoys : 194
[2023-09-16 07:26:27.856] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-16 07:26:29.389] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-16 07:26:30.151] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-16 07:27:12.135] [jointLog] [info] Thread saw mini-batch with a maximum of 4.74% zero probability fragments
[2023-09-16 07:27:12.148] [jointLog] [info] Thread saw mini-batch with a maximum of 4.70% zero probability fragments
[2023-09-16 07:27:12.221] [jointLog] [info] Thread saw mini-batch with a maximum of 4.66% zero probability fragments
[2023-09-16 07:27:12.236] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-09-16 07:27:12.292] [jointLog] [info] Thread saw mini-batch with a maximum of 4.66% zero probability fragments
[2023-09-16 07:27:12.338] [jointLog] [info] Thread saw mini-batch with a maximum of 4.94% zero probability fragments
[2023-09-16 07:27:12.356] [jointLog] [info] Thread saw mini-batch with a maximum of 4.82% zero probability fragments
[2023-09-16 07:27:12.378] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
[2023-09-16 07:27:12.668] [fileLog] [info] 
At end of round 0
==================
Observed 6539714 total fragments (6539714 in most recent round)

[2023-09-16 07:27:12.667] [jointLog] [info] Computed 217,252 rich equivalence classes for further processing
[2023-09-16 07:27:12.667] [jointLog] [info] Counted 5,933,570 total reads in the equivalence classes 
[2023-09-16 07:27:12.678] [jointLog] [info] Number of mappings discarded because of alignment score : 10,654,301
[2023-09-16 07:27:12.678] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 63,921
[2023-09-16 07:27:12.678] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 46,663
[2023-09-16 07:27:12.678] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-16 07:27:12.678] [jointLog] [info] Mapping rate = 90.7313%

[2023-09-16 07:27:12.678] [jointLog] [info] finished quantifyLibrary()
[2023-09-16 07:27:12.678] [jointLog] [info] Starting optimizer
[2023-09-16 07:27:18.498] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-16 07:27:18.870] [jointLog] [info] iteration = 0 | max rel diff. = 143.913
[2023-09-16 07:27:22.506] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-16 07:28:38.386] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-16 07:28:38.387] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-16 07:28:45.253] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-16 07:28:51.936] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-16 07:28:58.919] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-16 07:29:05.993] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-16 07:29:12.442] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-16 07:29:19.647] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-16 07:29:26.765] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-16 07:29:33.508] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-16 07:29:40.747] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-16 07:29:47.711] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 07:30:19.438] [jointLog] [info] iteration = 100 | max rel diff. = 9.49126
[2023-09-16 07:30:54.860] [jointLog] [info] iteration = 200 | max rel diff. = 17.8989
[2023-09-16 07:31:29.738] [jointLog] [info] iteration = 300 | max rel diff. = 1.7377
[2023-09-16 07:32:04.665] [jointLog] [info] iteration = 400 | max rel diff. = 9.9384
[2023-09-16 07:32:39.580] [jointLog] [info] iteration = 500 | max rel diff. = 5.6026
[2023-09-16 07:33:14.590] [jointLog] [info] iteration = 600 | max rel diff. = 0.451343
[2023-09-16 07:33:49.614] [jointLog] [info] iteration = 700 | max rel diff. = 0.493902
[2023-09-16 07:34:24.448] [jointLog] [info] iteration = 800 | max rel diff. = 0.246299
[2023-09-16 07:34:59.279] [jointLog] [info] iteration = 900 | max rel diff. = 0.125239
[2023-09-16 07:35:34.745] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.100718
[2023-09-16 07:36:10.393] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0132435
[2023-09-16 07:36:45.045] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0927896
[2023-09-16 07:37:19.621] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0315695
[2023-09-16 07:37:28.510] [jointLog] [info] iteration = 1,327 | max rel diff. = 0.00980711
[2023-09-16 07:37:30.640] [jointLog] [info] Finished optimizer
[2023-09-16 07:37:30.640] [jointLog] [info] writing output