[2022-05-27 09:39:56.448] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:56.448] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-05-27 09:39:56.448] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:56.448] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:56.448] [jointLog] [info] parsing read library format
[2022-05-27 09:39:56.448] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:56.449] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:56.449] [jointLog] [info] Loading dense pufferfish index.
[2022-05-27 09:39:56.509] [jointLog] [info] done
[2022-05-27 09:39:56.531] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:56.538] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:56.973] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-05-27 09:39:58.626] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments
[2022-05-27 09:39:58.631] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-05-27 09:39:58.730] [jointLog] [info] Thread saw mini-batch with a maximum of 1.02% zero probability fragments
[2022-05-27 09:39:58.740] [jointLog] [info] Thread saw mini-batch with a maximum of 1.04% zero probability fragments
[2022-05-27 09:39:58.786] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-05-27 09:39:58.808] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-05-27 09:39:58.890] [jointLog] [info] Computed 31983 rich equivalence classes for further processing
[2022-05-27 09:39:58.890] [jointLog] [info] Counted 282677 total reads in the equivalence classes 
[2022-05-27 09:39:58.894] [jointLog] [info] Number of mappings discarded because of alignment score : 75080
[2022-05-27 09:39:58.894] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9918
[2022-05-27 09:39:58.894] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:58.894] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 7564
[2022-05-27 09:39:58.898] [jointLog] [warning] Only 282677 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 09:39:58.898] [jointLog] [info] Mapping rate = 78.6006%

[2022-05-27 09:39:58.898] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:58.898] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:58.912] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:58.915] [jointLog] [info] iteration = 0 | max rel diff. = 780.457
[2022-05-27 09:39:59.082] [jointLog] [info] iteration = 100 | max rel diff. = 0.145292
[2022-05-27 09:39:58.891] [fileLog] [info] 
At end of round 0
==================
Observed 359637 total fragments (359637 in most recent round)

[2022-05-27 09:39:59.238] [jointLog] [info] iteration = 200 | max rel diff. = 0.936821
[2022-05-27 09:39:59.395] [jointLog] [info] iteration = 300 | max rel diff. = 0.0190692
[2022-05-27 09:39:59.551] [jointLog] [info] iteration = 400 | max rel diff. = 0.0112251
[2022-05-27 09:39:59.717] [jointLog] [info] iteration = 500 | max rel diff. = 0.112742
[2022-05-27 09:39:59.735] [jointLog] [info] iteration = 511 | max rel diff. = 0.00882499
[2022-05-27 09:39:59.736] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:59.736] [jointLog] [info] writing output