[2020-04-30 07:03:43.125] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:03:43.125] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:03:43.125] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:03:43.125] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:03:43.125] [jointLog] [info] parsing read library format
[2020-04-30 07:03:43.125] [jointLog] [info] There is 1 library.
[2020-04-30 07:03:43.201] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:03:43.201] [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 07:03:43.201] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:03:43.328] [jointLog] [info] done
[2020-04-30 07:03:43.328] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:03:43.344] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:03:44.126] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:03:45.472] [jointLog] [info] Computed 14,093 rich equivalence classes for further processing
[2020-04-30 07:03:45.472] [jointLog] [info] Counted 380,273 total reads in the equivalence classes 
[2020-04-30 07:03:45.484] [jointLog] [info] Number of mappings discarded because of alignment score : 211,758
[2020-04-30 07:03:45.484] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,352
[2020-04-30 07:03:45.484] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:03:45.484] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 589
[2020-04-30 07:03:45.487] [jointLog] [warning] Only 380273 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 07:03:45.487] [jointLog] [info] Mapping rate = 94.5689%

[2020-04-30 07:03:45.487] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:03:45.489] [jointLog] [info] Starting optimizer
[2020-04-30 07:03:45.504] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:03:45.505] [jointLog] [info] iteration = 0 | max rel diff. = 905.932
[2020-04-30 07:03:45.583] [jointLog] [info] iteration = 100 | max rel diff. = 15.2479
[2020-04-30 07:03:45.651] [jointLog] [info] iteration = 200 | max rel diff. = 0.0667936
[2020-04-30 07:03:45.714] [jointLog] [info] iteration = 300 | max rel diff. = 0.16758
[2020-04-30 07:03:45.753] [jointLog] [info] iteration = 364 | max rel diff. = 0.00776935
[2020-04-30 07:03:45.754] [jointLog] [info] Finished optimizer
[2020-04-30 07:03:45.754] [jointLog] [info] writing output 

[2020-04-30 07:03:45.473] [fileLog] [info] 
At end of round 0
==================
Observed 402112 total fragments (402112 in most recent round)