[2022-11-09 12:53:57.230] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 12:53:57.230] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 12:53:57.230] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 12:53:57.230] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 12:53:57.230] [jointLog] [info] parsing read library format
[2022-11-09 12:53:57.230] [jointLog] [info] There is 1 library.
[2022-11-09 12:53:57.231] [jointLog] [info] Loading pufferfish index
[2022-11-09 12:53:57.231] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 12:54:30.296] [jointLog] [info] done
[2022-11-09 12:54:30.340] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 12:54:30.697] [jointLog] [info] Number of decoys : 195
[2022-11-09 12:54:30.697] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 12:54:33.108] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:01:44.586] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:44.589] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:44.759] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:44.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:44.891] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:01:45.077] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:01:45.121] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:45.144] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:45.300] [jointLog] [info] Computed 103,868 rich equivalence classes for further processing
[2022-11-09 13:01:45.300] [jointLog] [info] Counted 3,491,598 total reads in the equivalence classes 
[2022-11-09 13:01:45.304] [jointLog] [info] Number of mappings discarded because of alignment score : 40,776,155
[2022-11-09 13:01:45.304] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,485,484
[2022-11-09 13:01:45.304] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 86,884
[2022-11-09 13:01:45.304] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,539,505
[2022-11-09 13:01:45.321] [jointLog] [warning] Only 3491598 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 13:01:45.321] [jointLog] [info] Mapping rate = 17.2791%

[2022-11-09 13:01:45.321] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:01:45.321] [jointLog] [info] Starting optimizer
[2022-11-09 13:01:45.411] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:01:45.427] [jointLog] [info] iteration = 0 | max rel diff. = 1816.07
[2022-11-09 13:01:45.300] [fileLog] [info] 
At end of round 0
==================
Observed 20207001 total fragments (20207001 in most recent round)

[2022-11-09 13:01:45.578] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:01:46.380] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:01:46.381] [jointLog] [info] processed bias for 0.1% of the transcripts
[2022-11-09 13:01:46.912] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:01:47.580] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:01:48.129] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:01:48.607] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 13:01:48.991] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:01:49.410] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:01:49.935] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:01:50.487] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:01:51.021] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:01:51.612] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:01:51.613] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:01:52.751] [jointLog] [info] iteration = 100 | max rel diff. = 18.9859
[2022-11-09 13:01:54.019] [jointLog] [info] iteration = 200 | max rel diff. = 13.0453
[2022-11-09 13:01:55.251] [jointLog] [info] iteration = 300 | max rel diff. = 3.31289
[2022-11-09 13:01:56.429] [jointLog] [info] iteration = 400 | max rel diff. = 6.91824
[2022-11-09 13:01:57.613] [jointLog] [info] iteration = 500 | max rel diff. = 0.0731924
[2022-11-09 13:01:58.652] [jointLog] [info] iteration = 600 | max rel diff. = 0.25566
[2022-11-09 13:01:59.740] [jointLog] [info] iteration = 700 | max rel diff. = 1.65049
[2022-11-09 13:02:00.865] [jointLog] [info] iteration = 800 | max rel diff. = 0.037314
[2022-11-09 13:02:01.966] [jointLog] [info] iteration = 900 | max rel diff. = 0.490325
[2022-11-09 13:02:02.789] [jointLog] [info] iteration = 979 | max rel diff. = 0.00970171
[2022-11-09 13:02:02.810] [jointLog] [info] Finished optimizer
[2022-11-09 13:02:02.810] [jointLog] [info] writing output