[2020-04-30 07:03:47.390] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:03:47.390] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:03:47.390] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:03:47.390] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:03:47.390] [jointLog] [info] parsing read library format
[2020-04-30 07:03:47.390] [jointLog] [info] There is 1 library.
[2020-04-30 07:03:47.457] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:03:47.457] [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 07:03:47.457] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:03:47.574] [jointLog] [info] done
[2020-04-30 07:03:47.574] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:03:47.590] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:03:48.263] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:03:50.672] [jointLog] [info] Computed 28,476 rich equivalence classes for further processing
[2020-04-30 07:03:50.672] [jointLog] [info] Counted 793,397 total reads in the equivalence classes 
[2020-04-30 07:03:50.684] [jointLog] [info] Number of mappings discarded because of alignment score : 276,234
[2020-04-30 07:03:50.684] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 17,554
[2020-04-30 07:03:50.684] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:03:50.684] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,573
[2020-04-30 07:03:50.687] [jointLog] [warning] Only 793397 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 07:03:50.687] [jointLog] [info] Mapping rate = 97.3227%

[2020-04-30 07:03:50.687] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:03:50.688] [jointLog] [info] Starting optimizer
[2020-04-30 07:03:50.702] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:03:50.704] [jointLog] [info] iteration = 0 | max rel diff. = 1901.91
[2020-04-30 07:03:50.804] [jointLog] [info] iteration = 100 | max rel diff. = 1.31233
[2020-04-30 07:03:50.892] [jointLog] [info] iteration = 200 | max rel diff. = 0.211411
[2020-04-30 07:03:50.974] [jointLog] [info] iteration = 300 | max rel diff. = 0.0504288
[2020-04-30 07:03:51.056] [jointLog] [info] iteration = 400 | max rel diff. = 7.6828
[2020-04-30 07:03:51.057] [jointLog] [info] iteration = 402 | max rel diff. = 0.00621768
[2020-04-30 07:03:51.058] [jointLog] [info] Finished optimizer
[2020-04-30 07:03:51.058] [jointLog] [info] writing output 

[2020-04-30 07:03:50.672] [fileLog] [info] 
At end of round 0
==================
Observed 815223 total fragments (815223 in most recent round)