[2022-11-09 13:09:56.709] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 13:09:56.709] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 13:09:56.709] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 13:09:56.709] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 13:09:56.709] [jointLog] [info] parsing read library format
[2022-11-09 13:09:56.709] [jointLog] [info] There is 1 library.
[2022-11-09 13:09:56.709] [jointLog] [info] Loading pufferfish index
[2022-11-09 13:09:56.710] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 13:10:18.829] [jointLog] [info] done
[2022-11-09 13:10:18.877] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 13:10:19.228] [jointLog] [info] Number of decoys : 195
[2022-11-09 13:10:19.228] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 13:10:22.694] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:16:34.132] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:16:34.168] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:16:34.187] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:16:34.289] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2022-11-09 13:16:34.462] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:16:34.541] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:16:34.743] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:16:34.759] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:16:34.950] [fileLog] [info] 
At end of round 0
==================
Observed 17364806 total fragments (17364806 in most recent round)

[2022-11-09 13:16:34.949] [jointLog] [info] Computed 102,755 rich equivalence classes for further processing
[2022-11-09 13:16:34.949] [jointLog] [info] Counted 3,056,605 total reads in the equivalence classes 
[2022-11-09 13:16:34.953] [jointLog] [info] Number of mappings discarded because of alignment score : 30,694,278
[2022-11-09 13:16:34.953] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,727,193
[2022-11-09 13:16:34.953] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 52,815
[2022-11-09 13:16:34.953] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,243,572
[2022-11-09 13:16:34.970] [jointLog] [warning] Only 3056605 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 13:16:34.970] [jointLog] [info] Mapping rate = 17.6023%

[2022-11-09 13:16:34.970] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:16:34.971] [jointLog] [info] Starting optimizer
[2022-11-09 13:16:35.065] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:16:35.079] [jointLog] [info] iteration = 0 | max rel diff. = 1597.21
[2022-11-09 13:16:35.227] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:16:36.075] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:16:36.076] [jointLog] [info] processed bias for 0.2% of the transcripts
[2022-11-09 13:16:36.670] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:16:37.239] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:16:37.793] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:16:38.366] [jointLog] [info] processed bias for 40.1% of the transcripts
[2022-11-09 13:16:38.669] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:16:39.016] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:16:39.527] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:16:40.062] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:16:40.612] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:16:41.150] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:16:41.157] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:16:42.337] [jointLog] [info] iteration = 100 | max rel diff. = 16.9269
[2022-11-09 13:16:43.631] [jointLog] [info] iteration = 200 | max rel diff. = 5.95089
[2022-11-09 13:16:44.957] [jointLog] [info] iteration = 300 | max rel diff. = 11.5648
[2022-11-09 13:16:46.219] [jointLog] [info] iteration = 400 | max rel diff. = 4.76204
[2022-11-09 13:16:47.482] [jointLog] [info] iteration = 500 | max rel diff. = 0.412795
[2022-11-09 13:16:48.770] [jointLog] [info] iteration = 600 | max rel diff. = 0.123293
[2022-11-09 13:16:50.052] [jointLog] [info] iteration = 700 | max rel diff. = 0.103374
[2022-11-09 13:16:51.322] [jointLog] [info] iteration = 800 | max rel diff. = 6.85686
[2022-11-09 13:16:52.635] [jointLog] [info] iteration = 900 | max rel diff. = 0.0144758
[2022-11-09 13:16:53.904] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.286307
[2022-11-09 13:16:55.188] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0205397
[2022-11-09 13:16:56.506] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.470058
[2022-11-09 13:16:57.409] [jointLog] [info] iteration = 1,269 | max rel diff. = 0.00686721
[2022-11-09 13:16:57.434] [jointLog] [info] Finished optimizer
[2022-11-09 13:16:57.434] [jointLog] [info] writing output