[2020-04-30 07:05:03.953] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:05:03.953] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:05:03.953] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:05:03.953] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:05:03.953] [jointLog] [info] parsing read library format
[2020-04-30 07:05:03.953] [jointLog] [info] There is 1 library.
[2020-04-30 07:05:04.022] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:05:04.022] [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 07:05:04.022] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:05:04.136] [jointLog] [info] done
[2020-04-30 07:05:04.136] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:05:04.152] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:05:04.936] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:05:10.610] [fileLog] [info] 
At end of round 0
==================
Observed 1567896 total fragments (1567896 in most recent round)

[2020-04-30 07:05:10.610] [jointLog] [info] Computed 15,755 rich equivalence classes for further processing
[2020-04-30 07:05:10.610] [jointLog] [info] Counted 1,546,941 total reads in the equivalence classes 
[2020-04-30 07:05:10.621] [jointLog] [info] Number of mappings discarded because of alignment score : 561,816
[2020-04-30 07:05:10.621] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,470
[2020-04-30 07:05:10.621] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:05:10.621] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,229
[2020-04-30 07:05:10.624] [jointLog] [warning] Only 1546941 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 07:05:10.624] [jointLog] [info] Mapping rate = 98.6635%

[2020-04-30 07:05:10.624] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:05:10.625] [jointLog] [info] Starting optimizer
[2020-04-30 07:05:10.641] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:05:10.642] [jointLog] [info] iteration = 0 | max rel diff. = 3610.58
[2020-04-30 07:05:10.744] [jointLog] [info] iteration = 100 | max rel diff. = 2.06392
[2020-04-30 07:05:10.815] [jointLog] [info] iteration = 200 | max rel diff. = 0.213994
[2020-04-30 07:05:10.879] [jointLog] [info] iteration = 300 | max rel diff. = 0.121073
[2020-04-30 07:05:10.944] [jointLog] [info] iteration = 400 | max rel diff. = 0.369173
[2020-04-30 07:05:11.008] [jointLog] [info] iteration = 500 | max rel diff. = 0.0286011
[2020-04-30 07:05:11.037] [jointLog] [info] iteration = 546 | max rel diff. = 0.00203337
[2020-04-30 07:05:11.038] [jointLog] [info] Finished optimizer
[2020-04-30 07:05:11.038] [jointLog] [info] writing output