[2022-11-09 12:47:29.641] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 12:47:29.641] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 12:47:29.641] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 12:47:29.641] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 12:47:29.641] [jointLog] [info] parsing read library format
[2022-11-09 12:47:29.641] [jointLog] [info] There is 1 library.
[2022-11-09 12:47:29.641] [jointLog] [info] Loading pufferfish index
[2022-11-09 12:47:29.641] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 12:48:03.745] [jointLog] [info] done
[2022-11-09 12:48:03.810] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 12:48:04.193] [jointLog] [info] Number of decoys : 195
[2022-11-09 12:48:04.193] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 12:48:07.308] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 12:53:27.904] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 12:53:28.004] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:53:28.124] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 12:53:28.184] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:53:28.236] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:53:28.258] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:53:28.259] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:53:28.685] [fileLog] [info] 
At end of round 0
==================
Observed 14987267 total fragments (14987267 in most recent round)

[2022-11-09 12:53:28.517] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:53:28.685] [jointLog] [info] Computed 98,506 rich equivalence classes for further processing
[2022-11-09 12:53:28.685] [jointLog] [info] Counted 2,627,319 total reads in the equivalence classes 
[2022-11-09 12:53:28.688] [jointLog] [info] Number of mappings discarded because of alignment score : 26,771,536
[2022-11-09 12:53:28.688] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,371,190
[2022-11-09 12:53:28.688] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 46,529
[2022-11-09 12:53:28.688] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,091,053
[2022-11-09 12:53:28.706] [jointLog] [warning] Only 2627319 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2022-11-09 12:53:28.706] [jointLog] [info] Mapping rate = 17.5303%

[2022-11-09 12:53:28.706] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 12:53:28.706] [jointLog] [info] Starting optimizer
[2022-11-09 12:53:28.796] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 12:53:28.810] [jointLog] [info] iteration = 0 | max rel diff. = 1387.03
[2022-11-09 12:53:28.948] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 12:53:29.731] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 12:53:29.731] [jointLog] [info] processed bias for 0.2% of the transcripts
[2022-11-09 12:53:30.260] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 12:53:30.779] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 12:53:31.346] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 12:53:31.942] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 12:53:32.484] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 12:53:33.010] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 12:53:33.554] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 12:53:33.905] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 12:53:34.118] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 12:53:34.612] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 12:53:34.613] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 12:53:35.621] [jointLog] [info] iteration = 100 | max rel diff. = 9.42242
[2022-11-09 12:53:36.772] [jointLog] [info] iteration = 200 | max rel diff. = 0.85565
[2022-11-09 12:53:37.930] [jointLog] [info] iteration = 300 | max rel diff. = 0.911752
[2022-11-09 12:53:39.137] [jointLog] [info] iteration = 400 | max rel diff. = 0.84618
[2022-11-09 12:53:40.332] [jointLog] [info] iteration = 500 | max rel diff. = 0.915234
[2022-11-09 12:53:41.554] [jointLog] [info] iteration = 600 | max rel diff. = 1.3201
[2022-11-09 12:53:42.785] [jointLog] [info] iteration = 700 | max rel diff. = 0.0563109
[2022-11-09 12:53:44.062] [jointLog] [info] iteration = 800 | max rel diff. = 0.0886776
[2022-11-09 12:53:45.257] [jointLog] [info] iteration = 900 | max rel diff. = 0.0144707
[2022-11-09 12:53:46.484] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0195372
[2022-11-09 12:53:47.794] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0339624
[2022-11-09 12:53:49.066] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0145571
[2022-11-09 12:53:50.300] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.589488
[2022-11-09 12:53:51.554] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0985242
[2022-11-09 12:53:51.686] [jointLog] [info] iteration = 1,412 | max rel diff. = 0.00642425
[2022-11-09 12:53:51.712] [jointLog] [info] Finished optimizer
[2022-11-09 12:53:51.712] [jointLog] [info] writing output