[2022-11-09 13:53:11.967] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 13:53:11.967] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 13:53:11.967] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 13:53:11.967] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 13:53:11.967] [jointLog] [info] parsing read library format
[2022-11-09 13:53:11.967] [jointLog] [info] There is 1 library.
[2022-11-09 13:53:11.967] [jointLog] [info] Loading pufferfish index
[2022-11-09 13:53:11.968] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 13:53:30.956] [jointLog] [info] done
[2022-11-09 13:53:31.000] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 13:53:31.376] [jointLog] [info] Number of decoys : 195
[2022-11-09 13:53:31.376] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 13:53:33.952] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:58:55.320] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:58:55.324] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:58:55.362] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:58:55.494] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:58:55.632] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:58:55.722] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:58:55.762] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:58:55.948] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:58:56.074] [jointLog] [info] Computed 107,269 rich equivalence classes for further processing
[2022-11-09 13:58:56.074] [jointLog] [info] Counted 3,426,797 total reads in the equivalence classes 
[2022-11-09 13:58:56.076] [jointLog] [info] Number of mappings discarded because of alignment score : 36,076,532
[2022-11-09 13:58:56.076] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,174,713
[2022-11-09 13:58:56.076] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 61,349
[2022-11-09 13:58:56.076] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,493,363
[2022-11-09 13:58:56.092] [jointLog] [warning] Only 3426797 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 13:58:56.092] [jointLog] [info] Mapping rate = 17.046%

[2022-11-09 13:58:56.092] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:58:56.092] [jointLog] [info] Starting optimizer
[2022-11-09 13:58:56.187] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:58:56.074] [fileLog] [info] 
At end of round 0
==================
Observed 20103287 total fragments (20103287 in most recent round)

[2022-11-09 13:58:56.207] [jointLog] [info] iteration = 0 | max rel diff. = 1795.51
[2022-11-09 13:58:56.327] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:58:56.854] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:58:56.854] [jointLog] [info] processed bias for 0.2% of the transcripts
[2022-11-09 13:58:57.184] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:58:57.524] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:58:57.845] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:58:58.195] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 13:58:58.495] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:58:58.745] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:58:58.937] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:58:59.150] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:58:59.465] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:58:59.802] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:59:00.862] [jointLog] [info] iteration = 100 | max rel diff. = 20.9294
[2022-11-09 13:59:02.016] [jointLog] [info] iteration = 200 | max rel diff. = 7.06585
[2022-11-09 13:59:03.174] [jointLog] [info] iteration = 300 | max rel diff. = 11.3206
[2022-11-09 13:59:04.319] [jointLog] [info] iteration = 400 | max rel diff. = 0.77367
[2022-11-09 13:59:05.501] [jointLog] [info] iteration = 500 | max rel diff. = 0.135431
[2022-11-09 13:59:06.661] [jointLog] [info] iteration = 600 | max rel diff. = 0.230381
[2022-11-09 13:59:07.815] [jointLog] [info] iteration = 700 | max rel diff. = 0.0653964
[2022-11-09 13:59:08.605] [jointLog] [info] iteration = 770 | max rel diff. = 0.00571091
[2022-11-09 13:59:08.626] [jointLog] [info] Finished optimizer
[2022-11-09 13:59:08.626] [jointLog] [info] writing output