[2020-04-30 07:03:34.337] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:03:34.337] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:03:34.337] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:03:34.337] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:03:34.337] [jointLog] [info] parsing read library format
[2020-04-30 07:03:34.337] [jointLog] [info] There is 1 library.
[2020-04-30 07:03:34.388] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:03:34.388] [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 07:03:34.388] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:03:34.505] [jointLog] [info] done
[2020-04-30 07:03:34.505] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:03:34.521] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:03:35.197] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:03:41.045] [jointLog] [info] Computed 23,317 rich equivalence classes for further processing
[2020-04-30 07:03:41.045] [jointLog] [info] Counted 1,954,258 total reads in the equivalence classes 
[2020-04-30 07:03:41.057] [jointLog] [info] Number of mappings discarded because of alignment score : 528,963
[2020-04-30 07:03:41.057] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,545
[2020-04-30 07:03:41.057] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:03:41.057] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,874
[2020-04-30 07:03:41.060] [jointLog] [warning] Only 1954258 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 07:03:41.060] [jointLog] [info] Mapping rate = 99.0268%

[2020-04-30 07:03:41.060] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:03:41.061] [jointLog] [info] Starting optimizer
[2020-04-30 07:03:41.077] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:03:41.079] [jointLog] [info] iteration = 0 | max rel diff. = 4641.55
[2020-04-30 07:03:41.169] [jointLog] [info] iteration = 100 | max rel diff. = 10.9424
[2020-04-30 07:03:41.249] [jointLog] [info] iteration = 200 | max rel diff. = 1.17574
[2020-04-30 07:03:41.325] [jointLog] [info] iteration = 300 | max rel diff. = 0.150236
[2020-04-30 07:03:41.369] [jointLog] [info] iteration = 359 | max rel diff. = 0.00536461
[2020-04-30 07:03:41.370] [jointLog] [info] Finished optimizer
[2020-04-30 07:03:41.370] [jointLog] [info] writing output 

[2020-04-30 07:03:41.046] [fileLog] [info] 
At end of round 0
==================
Observed 1973464 total fragments (1973464 in most recent round)