[2020-04-30 07:02:12.467] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:02:12.467] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:02:12.467] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:02:12.467] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:02:12.467] [jointLog] [info] parsing read library format
[2020-04-30 07:02:12.467] [jointLog] [info] There is 1 library.
[2020-04-30 07:02:12.544] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:02:12.544] [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 07:02:12.544] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:02:12.937] [jointLog] [info] done
[2020-04-30 07:02:12.937] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:02:12.964] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:02:13.915] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:02:19.970] [jointLog] [info] Computed 20,478 rich equivalence classes for further processing
[2020-04-30 07:02:19.970] [jointLog] [info] Counted 1,444,344 total reads in the equivalence classes 
[2020-04-30 07:02:19.984] [jointLog] [info] Number of mappings discarded because of alignment score : 476,424
[2020-04-30 07:02:19.984] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,553
[2020-04-30 07:02:19.984] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:02:19.984] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,556
[2020-04-30 07:02:19.988] [jointLog] [warning] Only 1444344 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 07:02:19.988] [jointLog] [info] Mapping rate = 99.1059%

[2020-04-30 07:02:19.988] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:02:19.989] [jointLog] [info] Starting optimizer
[2020-04-30 07:02:20.007] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:02:20.010] [jointLog] [info] iteration = 0 | max rel diff. = 3436.25
[2020-04-30 07:02:20.107] [jointLog] [info] iteration = 100 | max rel diff. = 5.38666
[2020-04-30 07:02:19.972] [fileLog] [info] 
At end of round 0
==================
Observed 1457375 total fragments (1457375 in most recent round)

[2020-04-30 07:02:20.192] [jointLog] [info] iteration = 200 | max rel diff. = 4.42195
[2020-04-30 07:02:20.273] [jointLog] [info] iteration = 300 | max rel diff. = 0.0190746
[2020-04-30 07:02:20.354] [jointLog] [info] iteration = 400 | max rel diff. = 0.0379255
[2020-04-30 07:02:20.428] [jointLog] [info] iteration = 500 | max rel diff. = 0.0367448
[2020-04-30 07:02:20.502] [jointLog] [info] iteration = 600 | max rel diff. = 0.0283916
[2020-04-30 07:02:20.529] [jointLog] [info] iteration = 637 | max rel diff. = 0.0082443
[2020-04-30 07:02:20.529] [jointLog] [info] Finished optimizer
[2020-04-30 07:02:20.529] [jointLog] [info] writing output