[2019-01-15 21:36:39.771] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-01-15 21:36:39.771] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-01-15 21:36:39.771] [jointLog] [info] parsing read library format
[2019-01-15 21:36:39.771] [jointLog] [info] There is 1 library.
[2019-01-15 21:36:39.873] [jointLog] [info] Loading Quasi index
[2019-01-15 21:36:39.874] [jointLog] [info] Loading 32-bit quasi index
[2019-01-15 21:36:47.959] [jointLog] [info] done
[2019-01-15 21:36:47.959] [jointLog] [info] Index contained 205,870 targets
[2019-01-15 21:36:50.733] [jointLog] [info] Automatically detected most likely library type as ISR
[2019-01-15 21:39:31.071] [jointLog] [info] Thread saw mini-batch with a maximum of 66.54% zero probability fragments
[2019-01-15 21:39:31.078] [jointLog] [info] Thread saw mini-batch with a maximum of 87.30% zero probability fragments
[2019-01-15 21:39:31.115] [jointLog] [info] Thread saw mini-batch with a maximum of 43.28% zero probability fragments
[2019-01-15 21:39:31.123] [jointLog] [info] Thread saw mini-batch with a maximum of 72.50% zero probability fragments
[2019-01-15 21:39:31.173] [jointLog] [info] Thread saw mini-batch with a maximum of 85.62% zero probability fragments
[2019-01-15 21:39:31.207] [jointLog] [info] Thread saw mini-batch with a maximum of 76.60% zero probability fragments
[2019-01-15 21:39:31.515] [jointLog] [info] Computed 345,402 rich equivalence classes for further processing
[2019-01-15 21:39:31.515] [jointLog] [info] Counted 37,805,027 total reads in the equivalence classes 
[2019-01-15 21:39:31.524] [jointLog] [info] Mapping rate = 88.8783%

[2019-01-15 21:39:31.524] [jointLog] [info] finished quantifyLibrary()
[2019-01-15 21:39:31.531] [jointLog] [info] Starting optimizer
[2019-01-15 21:39:31.652] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-15 21:39:31.671] [jointLog] [info] iteration = 0 | max rel diff. = 5181.69
[2019-01-15 21:39:31.867] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2019-01-15 21:39:31.516] [fileLog] [info] 
At end of round 0
==================
Observed 42535699 total fragments (42535699 in most recent round)

[2019-01-15 21:40:43.279] [jointLog] [info] Computed expected counts (for bias correction)
[2019-01-15 21:40:43.279] [jointLog] [info] processed bias for 0.0% of the transcripts
[2019-01-15 21:40:56.072] [jointLog] [info] processed bias for 10.0% of the transcripts
[2019-01-15 21:41:08.385] [jointLog] [info] processed bias for 20.0% of the transcripts
[2019-01-15 21:41:21.320] [jointLog] [info] processed bias for 30.0% of the transcripts
[2019-01-15 21:41:33.376] [jointLog] [info] processed bias for 40.0% of the transcripts
[2019-01-15 21:41:44.856] [jointLog] [info] processed bias for 50.0% of the transcripts
[2019-01-15 21:41:47.623] [jointLog] [info] processed bias for 100.0% of the transcripts
[2019-01-15 21:41:49.384] [jointLog] [info] iteration = 100 | max rel diff. = 15.3654
[2019-01-15 21:41:51.319] [jointLog] [info] iteration = 200 | max rel diff. = 2.96097
[2019-01-15 21:41:53.267] [jointLog] [info] iteration = 300 | max rel diff. = 1.21389
[2019-01-15 21:41:55.233] [jointLog] [info] iteration = 400 | max rel diff. = 4.04034
[2019-01-15 21:41:57.199] [jointLog] [info] iteration = 500 | max rel diff. = 2.55357
[2019-01-15 21:41:59.139] [jointLog] [info] iteration = 600 | max rel diff. = 0.149145
[2019-01-15 21:42:01.073] [jointLog] [info] iteration = 700 | max rel diff. = 8.32922
[2019-01-15 21:42:03.006] [jointLog] [info] iteration = 800 | max rel diff. = 0.159998
[2019-01-15 21:42:04.930] [jointLog] [info] iteration = 900 | max rel diff. = 0.0697759
[2019-01-15 21:42:06.855] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.686303
[2019-01-15 21:42:08.781] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0816195
[2019-01-15 21:42:09.466] [jointLog] [info] iteration = 1,136 | max rel diff. = 0.00860278
[2019-01-15 21:42:09.483] [jointLog] [info] Finished optimizer
[2019-01-15 21:42:09.483] [jointLog] [info] writing output 

[2019-01-15 21:42:09.902] [jointLog] [info] Starting Gibbs Sampler
[2019-01-15 21:42:49.346] [jointLog] [info] Finished Gibbs Sampler
