[2020-04-30 07:02:02.167] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:02:02.167] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:02:02.167] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:02:02.167] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:02:02.167] [jointLog] [info] parsing read library format
[2020-04-30 07:02:02.168] [jointLog] [info] There is 1 library.
[2020-04-30 07:02:02.313] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:02:02.325] [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 07:02:02.325] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:02:03.366] [jointLog] [info] done
[2020-04-30 07:02:03.366] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:02:03.394] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:02:04.112] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:02:09.847] [fileLog] [info] 
At end of round 0
==================
Observed 2298019 total fragments (2298019 in most recent round)

[2020-04-30 07:02:09.845] [jointLog] [info] Computed 29,560 rich equivalence classes for further processing
[2020-04-30 07:02:09.845] [jointLog] [info] Counted 2,280,001 total reads in the equivalence classes 
[2020-04-30 07:02:09.859] [jointLog] [info] Number of mappings discarded because of alignment score : 374,533
[2020-04-30 07:02:09.859] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 17,004
[2020-04-30 07:02:09.859] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:02:09.859] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,693
[2020-04-30 07:02:09.862] [jointLog] [warning] Only 2280001 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 07:02:09.862] [jointLog] [info] Mapping rate = 99.2159%

[2020-04-30 07:02:09.862] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:02:09.862] [jointLog] [info] Starting optimizer
[2020-04-30 07:02:09.880] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:02:09.881] [jointLog] [info] iteration = 0 | max rel diff. = 5257.12
[2020-04-30 07:02:09.980] [jointLog] [info] iteration = 100 | max rel diff. = 3.85996
[2020-04-30 07:02:10.064] [jointLog] [info] iteration = 200 | max rel diff. = 0.541331
[2020-04-30 07:02:10.145] [jointLog] [info] iteration = 300 | max rel diff. = 1.43929
[2020-04-30 07:02:10.227] [jointLog] [info] iteration = 400 | max rel diff. = 0.305201
[2020-04-30 07:02:10.308] [jointLog] [info] iteration = 500 | max rel diff. = 0.1238
[2020-04-30 07:02:10.389] [jointLog] [info] iteration = 600 | max rel diff. = 1.16644
[2020-04-30 07:02:10.470] [jointLog] [info] iteration = 700 | max rel diff. = 0.0468106
[2020-04-30 07:02:10.551] [jointLog] [info] iteration = 800 | max rel diff. = 0.05072
[2020-04-30 07:02:10.571] [jointLog] [info] iteration = 826 | max rel diff. = 0.00419771
[2020-04-30 07:02:10.572] [jointLog] [info] Finished optimizer
[2020-04-30 07:02:10.572] [jointLog] [info] writing output