[2022-05-27 09:39:46.128] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:46.129] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-05-27 09:39:46.129] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:46.129] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:46.129] [jointLog] [info] parsing read library format
[2022-05-27 09:39:46.129] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:46.129] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:46.129] [jointLog] [info] Loading dense pufferfish index.
[2022-05-27 09:39:46.192] [jointLog] [info] done
[2022-05-27 09:39:46.214] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:46.221] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:46.661] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-05-27 09:39:49.211] [jointLog] [info] Thread saw mini-batch with a maximum of 1.36% zero probability fragments
[2022-05-27 09:39:49.218] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments
[2022-05-27 09:39:49.234] [jointLog] [info] Thread saw mini-batch with a maximum of 1.24% zero probability fragments
[2022-05-27 09:39:49.241] [jointLog] [info] Thread saw mini-batch with a maximum of 1.12% zero probability fragments
[2022-05-27 09:39:49.241] [jointLog] [info] Thread saw mini-batch with a maximum of 1.26% zero probability fragments
[2022-05-27 09:39:49.260] [jointLog] [info] Thread saw mini-batch with a maximum of 1.34% zero probability fragments
[2022-05-27 09:39:49.350] [jointLog] [info] Computed 40088 rich equivalence classes for further processing
[2022-05-27 09:39:49.350] [jointLog] [info] Counted 423258 total reads in the equivalence classes 
[2022-05-27 09:39:49.354] [jointLog] [info] Number of mappings discarded because of alignment score : 94556
[2022-05-27 09:39:49.354] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16941
[2022-05-27 09:39:49.354] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:49.354] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 11202
[2022-05-27 09:39:49.356] [jointLog] [warning] Only 423258 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 09:39:49.356] [jointLog] [info] Mapping rate = 77.5378%

[2022-05-27 09:39:49.357] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:49.357] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:49.372] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:49.375] [jointLog] [info] iteration = 0 | max rel diff. = 1161.32
[2022-05-27 09:39:49.554] [jointLog] [info] iteration = 100 | max rel diff. = 0.940865
[2022-05-27 09:39:49.723] [jointLog] [info] iteration = 200 | max rel diff. = 0.266643
[2022-05-27 09:39:49.351] [fileLog] [info] 
At end of round 0
==================
Observed 545873 total fragments (545873 in most recent round)

[2022-05-27 09:39:49.834] [jointLog] [info] iteration = 267 | max rel diff. = 0.00102094
[2022-05-27 09:39:49.835] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:49.835] [jointLog] [info] writing output