[2020-04-26 09:05:18.049] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 09:05:18.049] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 09:05:18.049] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 09:05:18.049] [jointLog] [info] parsing read library format
[2020-04-26 09:05:18.049] [jointLog] [info] There is 1 library.
[2020-04-26 09:05:18.102] [jointLog] [info] Loading pufferfish index
[2020-04-26 09:05:18.102] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 09:05:18.218] [jointLog] [info] done
[2020-04-26 09:05:18.218] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 09:05:18.230] [jointLog] [info] Number of decoys : 0
[2020-04-26 09:05:23.929] [jointLog] [info] Computed 62,804 rich equivalence classes for further processing
[2020-04-26 09:05:23.929] [jointLog] [info] Counted 1,711,628 total reads in the equivalence classes 
[2020-04-26 09:05:23.948] [jointLog] [info] Number of mappings discarded because of alignment score : 553,510
[2020-04-26 09:05:23.948] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,872
[2020-04-26 09:05:23.948] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 09:05:23.948] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,511
[2020-04-26 09:05:23.951] [jointLog] [warning] Only 1711628 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-26 09:05:23.951] [jointLog] [info] Mapping rate = 98.9712%

[2020-04-26 09:05:23.951] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 09:05:23.952] [jointLog] [info] Starting optimizer
[2020-04-26 09:05:23.970] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 09:05:23.975] [jointLog] [info] iteration = 0 | max rel diff. = 4012.37
[2020-04-26 09:05:23.929] [fileLog] [info] 
At end of round 0
==================
Observed 1729420 total fragments (1729420 in most recent round)

[2020-04-26 09:05:24.231] [jointLog] [info] iteration = 100 | max rel diff. = 9.24718
[2020-04-26 09:05:24.489] [jointLog] [info] iteration = 200 | max rel diff. = 1.82856
[2020-04-26 09:05:24.753] [jointLog] [info] iteration = 300 | max rel diff. = 0.885471
[2020-04-26 09:05:25.012] [jointLog] [info] iteration = 400 | max rel diff. = 0.0559703
[2020-04-26 09:05:25.271] [jointLog] [info] iteration = 500 | max rel diff. = 0.552296
[2020-04-26 09:05:25.279] [jointLog] [info] iteration = 504 | max rel diff. = 0.00391797
[2020-04-26 09:05:25.280] [jointLog] [info] Finished optimizer
[2020-04-26 09:05:25.280] [jointLog] [info] writing output