[2022-11-09 13:02:07.664] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 13:02:07.664] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 13:02:07.664] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 13:02:07.664] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 13:02:07.664] [jointLog] [info] parsing read library format
[2022-11-09 13:02:07.664] [jointLog] [info] There is 1 library.
[2022-11-09 13:02:07.664] [jointLog] [info] Loading pufferfish index
[2022-11-09 13:02:07.664] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 13:02:39.423] [jointLog] [info] done
[2022-11-09 13:02:39.466] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 13:02:39.820] [jointLog] [info] Number of decoys : 195
[2022-11-09 13:02:39.820] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 13:02:42.564] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:09:21.294] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:09:21.310] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:21.421] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:21.666] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:21.757] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:21.877] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:21.934] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:22.000] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:22.176] [jointLog] [info] Computed 102,706 rich equivalence classes for further processing
[2022-11-09 13:09:22.176] [jointLog] [info] Counted 3,047,166 total reads in the equivalence classes 
[2022-11-09 13:09:22.180] [jointLog] [info] Number of mappings discarded because of alignment score : 35,453,597
[2022-11-09 13:09:22.180] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,068,445
[2022-11-09 13:09:22.180] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 62,791
[2022-11-09 13:09:22.180] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,530,170
[2022-11-09 13:09:22.197] [jointLog] [warning] Only 3047166 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 13:09:22.197] [jointLog] [info] Mapping rate = 16.4306%

[2022-11-09 13:09:22.197] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:09:22.197] [jointLog] [info] Starting optimizer
[2022-11-09 13:09:22.287] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:09:22.301] [jointLog] [info] iteration = 0 | max rel diff. = 1573.41
[2022-11-09 13:09:22.177] [fileLog] [info] 
At end of round 0
==================
Observed 18545652 total fragments (18545652 in most recent round)

[2022-11-09 13:09:22.435] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:09:23.184] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:09:23.184] [jointLog] [info] processed bias for 0.1% of the transcripts
[2022-11-09 13:09:23.734] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:09:24.297] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:09:24.827] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:09:25.384] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 13:09:25.940] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:09:26.295] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:09:26.637] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:09:26.963] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:09:27.475] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:09:28.011] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:09:28.015] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:09:29.123] [jointLog] [info] iteration = 100 | max rel diff. = 10.3164
[2022-11-09 13:09:30.318] [jointLog] [info] iteration = 200 | max rel diff. = 4.05514
[2022-11-09 13:09:31.435] [jointLog] [info] iteration = 300 | max rel diff. = 1.26137
[2022-11-09 13:09:32.702] [jointLog] [info] iteration = 400 | max rel diff. = 4.83459
[2022-11-09 13:09:33.902] [jointLog] [info] iteration = 500 | max rel diff. = 0.714856
[2022-11-09 13:09:35.107] [jointLog] [info] iteration = 600 | max rel diff. = 0.100178
[2022-11-09 13:09:36.328] [jointLog] [info] iteration = 700 | max rel diff. = 0.0403561
[2022-11-09 13:09:37.553] [jointLog] [info] iteration = 800 | max rel diff. = 0.185922
[2022-11-09 13:09:38.718] [jointLog] [info] iteration = 900 | max rel diff. = 0.0937591
[2022-11-09 13:09:39.846] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0364115
[2022-11-09 13:09:40.846] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0436833
[2022-11-09 13:09:41.565] [jointLog] [info] iteration = 1,169 | max rel diff. = 0.00684957
[2022-11-09 13:09:41.588] [jointLog] [info] Finished optimizer
[2022-11-09 13:09:41.588] [jointLog] [info] writing output