[2023-09-08 16:17:27.177] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-08 16:17:27.177] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-08 16:17:27.177] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-08 16:17:27.177] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-08 16:17:27.177] [jointLog] [info] parsing read library format
[2023-09-08 16:17:27.177] [jointLog] [info] There is 1 library.
[2023-09-08 16:17:27.177] [jointLog] [info] Loading pufferfish index
[2023-09-08 16:17:27.177] [jointLog] [info] Loading dense pufferfish index.
[2023-09-08 16:18:37.449] [jointLog] [info] done
[2023-09-08 16:18:37.569] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-08 16:19:14.736] [jointLog] [info] Number of decoys : 194
[2023-09-08 16:19:14.736] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-08 16:19:17.559] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-08 16:27:21.221] [jointLog] [info] Thread saw mini-batch with a maximum of 6.06% zero probability fragments
[2023-09-08 16:27:21.255] [jointLog] [info] Thread saw mini-batch with a maximum of 6.16% zero probability fragments
[2023-09-08 16:27:21.305] [jointLog] [info] Thread saw mini-batch with a maximum of 6.08% zero probability fragments
[2023-09-08 16:27:21.383] [jointLog] [info] Thread saw mini-batch with a maximum of 6.08% zero probability fragments
[2023-09-08 16:27:21.553] [jointLog] [info] Thread saw mini-batch with a maximum of 6.22% zero probability fragments
[2023-09-08 16:27:21.630] [jointLog] [info] Thread saw mini-batch with a maximum of 5.96% zero probability fragments
[2023-09-08 16:27:21.707] [jointLog] [info] Thread saw mini-batch with a maximum of 6.00% zero probability fragments
[2023-09-08 16:27:21.858] [jointLog] [info] Thread saw mini-batch with a maximum of 6.08% zero probability fragments
[2023-09-08 16:27:22.374] [fileLog] [info] 
At end of round 0
==================
Observed 37734675 total fragments (37734675 in most recent round)

[2023-09-08 16:27:22.373] [jointLog] [info] Computed 320,452 rich equivalence classes for further processing
[2023-09-08 16:27:22.373] [jointLog] [info] Counted 31,380,791 total reads in the equivalence classes 
[2023-09-08 16:27:22.382] [jointLog] [warning] 0.000238507% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 30.


[2023-09-08 16:27:22.382] [jointLog] [info] Number of mappings discarded because of alignment score : 9,338,808
[2023-09-08 16:27:22.382] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,845,047
[2023-09-08 16:27:22.382] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 3,039,985
[2023-09-08 16:27:22.382] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,439,246
[2023-09-08 16:27:22.382] [jointLog] [info] Mapping rate = 83.1617%

[2023-09-08 16:27:22.382] [jointLog] [info] finished quantifyLibrary()
[2023-09-08 16:27:22.382] [jointLog] [info] Starting optimizer
[2023-09-08 16:27:27.089] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-08 16:27:27.417] [jointLog] [info] iteration = 0 | max rel diff. = 408.917
[2023-09-08 16:27:30.733] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-08 16:32:51.128] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-08 16:32:51.129] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-08 16:33:17.003] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-08 16:33:42.263] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-08 16:34:08.998] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-08 16:34:35.778] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-08 16:35:01.748] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-08 16:35:27.491] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-08 16:35:53.357] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-08 16:36:18.554] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-08 16:36:44.409] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-08 16:37:10.236] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-08 16:37:41.069] [jointLog] [info] iteration = 100 | max rel diff. = 15.8837
[2023-09-08 16:38:14.960] [jointLog] [info] iteration = 200 | max rel diff. = 9.04647
[2023-09-08 16:38:48.235] [jointLog] [info] iteration = 300 | max rel diff. = 15.2798
[2023-09-08 16:39:21.895] [jointLog] [info] iteration = 400 | max rel diff. = 5.87384
[2023-09-08 16:39:55.231] [jointLog] [info] iteration = 500 | max rel diff. = 0.548156
[2023-09-08 16:40:29.005] [jointLog] [info] iteration = 600 | max rel diff. = 1.54469
[2023-09-08 16:41:02.648] [jointLog] [info] iteration = 700 | max rel diff. = 12.0635
[2023-09-08 16:41:36.718] [jointLog] [info] iteration = 800 | max rel diff. = 0.0759024
[2023-09-08 16:42:10.474] [jointLog] [info] iteration = 900 | max rel diff. = 0.0597167
[2023-09-08 16:42:44.388] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0323542
[2023-09-08 16:43:18.291] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0454374
[2023-09-08 16:43:51.982] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0279938
[2023-09-08 16:44:10.366] [jointLog] [info] iteration = 1,255 | max rel diff. = 0.00289284
[2023-09-08 16:44:12.230] [jointLog] [info] Finished optimizer
[2023-09-08 16:44:12.230] [jointLog] [info] writing output