[2020-04-30 07:04:11.735] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:11.735] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:11.735] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:11.735] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:11.735] [jointLog] [info] parsing read library format
[2020-04-30 07:04:11.735] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:11.809] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:11.809] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information.
[2020-04-30 07:04:11.809] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:11.927] [jointLog] [info] done
[2020-04-30 07:04:11.927] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:11.943] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:12.629] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:04:12.908] [fileLog] [info] 
At end of round 0
==================
Observed 91614 total fragments (91614 in most recent round)

[2020-04-30 07:04:12.907] [jointLog] [info] Computed 12,887 rich equivalence classes for further processing
[2020-04-30 07:04:12.907] [jointLog] [info] Counted 79,579 total reads in the equivalence classes 
[2020-04-30 07:04:12.940] [jointLog] [info] Number of mappings discarded because of alignment score : 76,381
[2020-04-30 07:04:12.940] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,405
[2020-04-30 07:04:12.940] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:12.940] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 250
[2020-04-30 07:04:12.944] [jointLog] [warning] Only 79579 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-30 07:04:12.944] [jointLog] [info] Mapping rate = 86.8634%

[2020-04-30 07:04:12.944] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:12.945] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:12.959] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:12.962] [jointLog] [info] iteration = 0 | max rel diff. = 190.712
[2020-04-30 07:04:13.044] [jointLog] [info] iteration = 100 | max rel diff. = 0.298364
[2020-04-30 07:04:13.115] [jointLog] [info] iteration = 200 | max rel diff. = 0.16591
[2020-04-30 07:04:13.147] [jointLog] [info] iteration = 248 | max rel diff. = 0.00949298
[2020-04-30 07:04:13.148] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:13.148] [jointLog] [info] writing output