[2020-04-30 07:03:28.060] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:03:28.060] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:03:28.060] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:03:28.060] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:03:28.060] [jointLog] [info] parsing read library format
[2020-04-30 07:03:28.060] [jointLog] [info] There is 1 library.
[2020-04-30 07:03:28.127] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:03:28.127] [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 07:03:28.127] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:03:28.276] [jointLog] [info] done
[2020-04-30 07:03:28.276] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:03:28.292] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:03:28.835] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:03:32.122] [jointLog] [info] Computed 25,813 rich equivalence classes for further processing
[2020-04-30 07:03:32.122] [jointLog] [info] Counted 1,346,110 total reads in the equivalence classes 
[2020-04-30 07:03:32.135] [jointLog] [info] Number of mappings discarded because of alignment score : 272,233
[2020-04-30 07:03:32.135] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,962
[2020-04-30 07:03:32.135] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:03:32.135] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,352
[2020-04-30 07:03:32.138] [jointLog] [warning] Only 1346110 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 07:03:32.138] [jointLog] [info] Mapping rate = 98.924%

[2020-04-30 07:03:32.138] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:03:32.139] [jointLog] [info] Starting optimizer
[2020-04-30 07:03:32.152] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:03:32.154] [jointLog] [info] iteration = 0 | max rel diff. = 2858.26
[2020-04-30 07:03:32.123] [fileLog] [info] 
At end of round 0
==================
Observed 1360752 total fragments (1360752 in most recent round)

[2020-04-30 07:03:32.248] [jointLog] [info] iteration = 100 | max rel diff. = 7.30647
[2020-04-30 07:03:32.330] [jointLog] [info] iteration = 200 | max rel diff. = 1.05557
[2020-04-30 07:03:32.408] [jointLog] [info] iteration = 300 | max rel diff. = 0.0419766
[2020-04-30 07:03:32.485] [jointLog] [info] iteration = 400 | max rel diff. = 0.71107
[2020-04-30 07:03:32.563] [jointLog] [info] iteration = 500 | max rel diff. = 0.026917
[2020-04-30 07:03:32.631] [jointLog] [info] iteration = 589 | max rel diff. = 0.00445131
[2020-04-30 07:03:32.632] [jointLog] [info] Finished optimizer
[2020-04-30 07:03:32.632] [jointLog] [info] writing output