[2020-04-30 07:04:14.979] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:14.979] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:14.979] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:14.979] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:14.979] [jointLog] [info] parsing read library format
[2020-04-30 07:04:14.979] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:15.047] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:15.047] [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 07:04:15.047] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:15.162] [jointLog] [info] done
[2020-04-30 07:04:15.162] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:15.179] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:15.866] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:04:24.811] [jointLog] [info] Computed 29,239 rich equivalence classes for further processing
[2020-04-30 07:04:24.811] [jointLog] [info] Counted 3,198,705 total reads in the equivalence classes 
[2020-04-30 07:04:24.823] [jointLog] [info] Number of mappings discarded because of alignment score : 863,773
[2020-04-30 07:04:24.823] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,206
[2020-04-30 07:04:24.823] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:24.823] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,541
[2020-04-30 07:04:24.826] [jointLog] [warning] Only 3198705 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 07:04:24.826] [jointLog] [info] Mapping rate = 99.2723%

[2020-04-30 07:04:24.826] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:24.827] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:24.845] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:24.847] [jointLog] [info] iteration = 0 | max rel diff. = 7222.41
[2020-04-30 07:04:24.969] [jointLog] [info] iteration = 100 | max rel diff. = 15.3561
[2020-04-30 07:04:25.060] [jointLog] [info] iteration = 200 | max rel diff. = 10.0546
[2020-04-30 07:04:25.150] [jointLog] [info] iteration = 300 | max rel diff. = 0.044478
[2020-04-30 07:04:24.812] [fileLog] [info] 
At end of round 0
==================
Observed 3222151 total fragments (3222151 in most recent round)

[2020-04-30 07:04:25.240] [jointLog] [info] iteration = 400 | max rel diff. = 0.39081
[2020-04-30 07:04:25.329] [jointLog] [info] iteration = 500 | max rel diff. = 0.122808
[2020-04-30 07:04:25.419] [jointLog] [info] iteration = 600 | max rel diff. = 0.543473
[2020-04-30 07:04:25.506] [jointLog] [info] iteration = 700 | max rel diff. = 0.0530419
[2020-04-30 07:04:25.587] [jointLog] [info] iteration = 800 | max rel diff. = 0.0262999
[2020-04-30 07:04:25.618] [jointLog] [info] iteration = 838 | max rel diff. = 0.00612989
[2020-04-30 07:04:25.618] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:25.618] [jointLog] [info] writing output