[2020-04-30 07:02:22.257] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:02:22.257] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:02:22.257] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:02:22.257] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:02:22.257] [jointLog] [info] parsing read library format
[2020-04-30 07:02:22.258] [jointLog] [info] There is 1 library.
[2020-04-30 07:02:22.322] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:02:22.322] [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 07:02:22.322] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:02:22.434] [jointLog] [info] done
[2020-04-30 07:02:22.434] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:02:22.450] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:02:23.039] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:02:28.994] [jointLog] [info] Computed 30,255 rich equivalence classes for further processing
[2020-04-30 07:02:28.994] [jointLog] [info] Counted 2,320,962 total reads in the equivalence classes 
[2020-04-30 07:02:29.006] [jointLog] [info] Number of mappings discarded because of alignment score : 439,216
[2020-04-30 07:02:29.006] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,284
[2020-04-30 07:02:29.006] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:02:29.006] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,506
[2020-04-30 07:02:29.009] [jointLog] [warning] Only 2320962 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 07:02:29.009] [jointLog] [info] Mapping rate = 99.2551%

[2020-04-30 07:02:29.009] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:02:29.011] [jointLog] [info] Starting optimizer
[2020-04-30 07:02:29.027] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:02:29.029] [jointLog] [info] iteration = 0 | max rel diff. = 4876.02
[2020-04-30 07:02:29.153] [jointLog] [info] iteration = 100 | max rel diff. = 15.1856
[2020-04-30 07:02:29.238] [jointLog] [info] iteration = 200 | max rel diff. = 2.09506
[2020-04-30 07:02:29.319] [jointLog] [info] iteration = 300 | max rel diff. = 0.631201
[2020-04-30 07:02:29.401] [jointLog] [info] iteration = 400 | max rel diff. = 0.0474015
[2020-04-30 07:02:28.995] [fileLog] [info] 
At end of round 0
==================
Observed 2338381 total fragments (2338381 in most recent round)

[2020-04-30 07:02:29.482] [jointLog] [info] iteration = 500 | max rel diff. = 0.208421
[2020-04-30 07:02:29.564] [jointLog] [info] iteration = 600 | max rel diff. = 0.693294
[2020-04-30 07:02:29.645] [jointLog] [info] iteration = 700 | max rel diff. = 0.812229
[2020-04-30 07:02:29.727] [jointLog] [info] iteration = 800 | max rel diff. = 0.0262918
[2020-04-30 07:02:29.803] [jointLog] [info] iteration = 894 | max rel diff. = 0.00757559
[2020-04-30 07:02:29.804] [jointLog] [info] Finished optimizer
[2020-04-30 07:02:29.804] [jointLog] [info] writing output