[2022-05-27 09:39:35.337] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:35.337] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-05-27 09:39:35.337] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:35.337] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:35.337] [jointLog] [info] parsing read library format
[2022-05-27 09:39:35.337] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:35.337] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:35.337] [jointLog] [info] Loading dense pufferfish index.
[2022-05-27 09:39:35.398] [jointLog] [info] done
[2022-05-27 09:39:35.419] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:35.427] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:35.791] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-05-27 09:39:38.200] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-05-27 09:39:38.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-05-27 09:39:38.226] [jointLog] [info] Thread saw mini-batch with a maximum of 1.12% zero probability fragments
[2022-05-27 09:39:38.275] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-05-27 09:39:38.289] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-05-27 09:39:38.306] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-05-27 09:39:38.386] [jointLog] [info] Computed 26222 rich equivalence classes for further processing
[2022-05-27 09:39:38.386] [jointLog] [info] Counted 451182 total reads in the equivalence classes 
[2022-05-27 09:39:38.390] [jointLog] [info] Number of mappings discarded because of alignment score : 56158
[2022-05-27 09:39:38.390] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 10836
[2022-05-27 09:39:38.390] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:38.390] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 11963
[2022-05-27 09:39:38.393] [jointLog] [warning] Only 451182 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2022-05-27 09:39:38.393] [jointLog] [info] Mapping rate = 90.2364%

[2022-05-27 09:39:38.393] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:38.393] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:38.407] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:38.409] [jointLog] [info] iteration = 0 | max rel diff. = 1276.79
[2022-05-27 09:39:38.386] [fileLog] [info] 
At end of round 0
==================
Observed 500000 total fragments (500000 in most recent round)

[2022-05-27 09:39:38.571] [jointLog] [info] iteration = 100 | max rel diff. = 1.24167
[2022-05-27 09:39:38.720] [jointLog] [info] iteration = 200 | max rel diff. = 0.20455
[2022-05-27 09:39:38.870] [jointLog] [info] iteration = 300 | max rel diff. = 0.528338
[2022-05-27 09:39:38.966] [jointLog] [info] iteration = 365 | max rel diff. = 0.00778503
[2022-05-27 09:39:38.967] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:38.967] [jointLog] [info] writing output