[2020-04-30 07:03:16.762] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:03:16.762] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:03:16.762] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:03:16.762] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:03:16.762] [jointLog] [info] parsing read library format
[2020-04-30 07:03:16.762] [jointLog] [info] There is 1 library.
[2020-04-30 07:03:16.854] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:03:16.854] [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 07:03:16.854] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:03:16.998] [jointLog] [info] done
[2020-04-30 07:03:16.998] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:03:17.014] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:03:17.821] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:03:26.045] [jointLog] [info] Computed 14,142 rich equivalence classes for further processing
[2020-04-30 07:03:26.045] [jointLog] [info] Counted 2,610,801 total reads in the equivalence classes 
[2020-04-30 07:03:26.057] [jointLog] [info] Number of mappings discarded because of alignment score : 828,701
[2020-04-30 07:03:26.057] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,911
[2020-04-30 07:03:26.057] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:03:26.057] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,619
[2020-04-30 07:03:26.060] [jointLog] [warning] Only 2610801 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 07:03:26.060] [jointLog] [info] Mapping rate = 99.1818%

[2020-04-30 07:03:26.060] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:03:26.061] [jointLog] [info] Starting optimizer
[2020-04-30 07:03:26.075] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:03:26.078] [jointLog] [info] iteration = 0 | max rel diff. = 5797.17
[2020-04-30 07:03:26.156] [jointLog] [info] iteration = 100 | max rel diff. = 11.9299
[2020-04-30 07:03:26.223] [jointLog] [info] iteration = 200 | max rel diff. = 3.52464
[2020-04-30 07:03:26.284] [jointLog] [info] iteration = 300 | max rel diff. = 2.25293
[2020-04-30 07:03:26.345] [jointLog] [info] iteration = 400 | max rel diff. = 0.033746
[2020-04-30 07:03:26.379] [jointLog] [info] iteration = 456 | max rel diff. = 0.00325304
[2020-04-30 07:03:26.380] [jointLog] [info] Finished optimizer
[2020-04-30 07:03:26.380] [jointLog] [info] writing output 

[2020-04-30 07:03:26.046] [fileLog] [info] 
At end of round 0
==================
Observed 2632340 total fragments (2632340 in most recent round)