[2020-04-30 07:04:33.766] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:33.766] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:33.766] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:33.766] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:33.766] [jointLog] [info] parsing read library format
[2020-04-30 07:04:33.766] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:33.833] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:33.833] [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 07:04:33.833] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:33.950] [jointLog] [info] done
[2020-04-30 07:04:33.950] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:33.966] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:34.635] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:04:41.382] [fileLog] [info] 
At end of round 0
==================
Observed 2563755 total fragments (2563755 in most recent round)

[2020-04-30 07:04:41.382] [jointLog] [info] Computed 29,322 rich equivalence classes for further processing
[2020-04-30 07:04:41.382] [jointLog] [info] Counted 2,538,058 total reads in the equivalence classes 
[2020-04-30 07:04:41.393] [jointLog] [info] Number of mappings discarded because of alignment score : 599,504
[2020-04-30 07:04:41.393] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,790
[2020-04-30 07:04:41.393] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:41.393] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,104
[2020-04-30 07:04:41.397] [jointLog] [warning] Only 2538058 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 07:04:41.397] [jointLog] [info] Mapping rate = 98.9977%

[2020-04-30 07:04:41.397] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:41.398] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:41.413] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:41.415] [jointLog] [info] iteration = 0 | max rel diff. = 5952.2
[2020-04-30 07:04:41.515] [jointLog] [info] iteration = 100 | max rel diff. = 8.17616
[2020-04-30 07:04:41.601] [jointLog] [info] iteration = 200 | max rel diff. = 13.7999
[2020-04-30 07:04:41.682] [jointLog] [info] iteration = 300 | max rel diff. = 4.29595
[2020-04-30 07:04:41.763] [jointLog] [info] iteration = 400 | max rel diff. = 0.243642
[2020-04-30 07:04:41.844] [jointLog] [info] iteration = 500 | max rel diff. = 0.0866499
[2020-04-30 07:04:41.925] [jointLog] [info] iteration = 600 | max rel diff. = 0.0802483
[2020-04-30 07:04:42.005] [jointLog] [info] iteration = 700 | max rel diff. = 0.0693964
[2020-04-30 07:04:42.086] [jointLog] [info] iteration = 800 | max rel diff. = 0.884456
[2020-04-30 07:04:42.167] [jointLog] [info] iteration = 900 | max rel diff. = 0.815251
[2020-04-30 07:04:42.247] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.148547
[2020-04-30 07:04:42.328] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.604452
[2020-04-30 07:04:42.396] [jointLog] [info] iteration = 1,186 | max rel diff. = 0.00376349
[2020-04-30 07:04:42.397] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:42.397] [jointLog] [info] writing output