[2019-01-15 21:36:10.012] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-01-15 21:36:10.012] [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 21:36:10.012] [jointLog] [info] parsing read library format
[2019-01-15 21:36:10.012] [jointLog] [info] There is 1 library.
[2019-01-15 21:36:10.057] [jointLog] [info] Loading Quasi index
[2019-01-15 21:36:10.058] [jointLog] [info] Loading 32-bit quasi index
[2019-01-15 21:36:22.402] [jointLog] [info] done
[2019-01-15 21:36:22.402] [jointLog] [info] Index contained 205,870 targets
[2019-01-15 21:36:26.222] [jointLog] [info] Automatically detected most likely library type as ISR
[2019-01-15 21:39:06.241] [jointLog] [info] Thread saw mini-batch with a maximum of 86.28% zero probability fragments
[2019-01-15 21:39:06.361] [jointLog] [info] Thread saw mini-batch with a maximum of 85.00% zero probability fragments
[2019-01-15 21:39:06.368] [jointLog] [info] Thread saw mini-batch with a maximum of 66.90% zero probability fragments
[2019-01-15 21:39:06.375] [jointLog] [info] Thread saw mini-batch with a maximum of 76.40% zero probability fragments
[2019-01-15 21:39:06.451] [jointLog] [info] Thread saw mini-batch with a maximum of 63.24% zero probability fragments
[2019-01-15 21:39:06.458] [jointLog] [info] Thread saw mini-batch with a maximum of 74.46% zero probability fragments
[2019-01-15 21:39:06.763] [jointLog] [info] Computed 316,480 rich equivalence classes for further processing
[2019-01-15 21:39:06.763] [jointLog] [info] Counted 38,244,703 total reads in the equivalence classes 
[2019-01-15 21:39:06.773] [jointLog] [info] Mapping rate = 89.5238%

[2019-01-15 21:39:06.773] [jointLog] [info] finished quantifyLibrary()
[2019-01-15 21:39:06.787] [jointLog] [info] Starting optimizer
[2019-01-15 21:39:06.922] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-15 21:39:06.946] [jointLog] [info] iteration = 0 | max rel diff. = 4752.84
[2019-01-15 21:39:06.764] [fileLog] [info] 
At end of round 0
==================
Observed 42720174 total fragments (42720174 in most recent round)

[2019-01-15 21:39:07.194] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2019-01-15 21:40:27.782] [jointLog] [info] Computed expected counts (for bias correction)
[2019-01-15 21:40:27.783] [jointLog] [info] processed bias for 0.0% of the transcripts
[2019-01-15 21:40:43.860] [jointLog] [info] processed bias for 10.0% of the transcripts
[2019-01-15 21:40:57.517] [jointLog] [info] processed bias for 20.0% of the transcripts
[2019-01-15 21:41:14.776] [jointLog] [info] processed bias for 30.0% of the transcripts
[2019-01-15 21:41:30.899] [jointLog] [info] processed bias for 40.0% of the transcripts
[2019-01-15 21:41:46.305] [jointLog] [info] processed bias for 50.0% of the transcripts
[2019-01-15 21:41:46.972] [jointLog] [info] processed bias for 100.0% of the transcripts
[2019-01-15 21:41:48.733] [jointLog] [info] iteration = 100 | max rel diff. = 12.303
[2019-01-15 21:41:50.634] [jointLog] [info] iteration = 200 | max rel diff. = 9.12154
[2019-01-15 21:41:52.642] [jointLog] [info] iteration = 300 | max rel diff. = 9.7529
[2019-01-15 21:41:54.626] [jointLog] [info] iteration = 400 | max rel diff. = 3.18434
[2019-01-15 21:41:56.635] [jointLog] [info] iteration = 500 | max rel diff. = 0.22371
[2019-01-15 21:41:58.842] [jointLog] [info] iteration = 600 | max rel diff. = 0.301249
[2019-01-15 21:42:00.879] [jointLog] [info] iteration = 700 | max rel diff. = 4.48691
[2019-01-15 21:42:02.688] [jointLog] [info] iteration = 800 | max rel diff. = 0.0955849
[2019-01-15 21:42:05.062] [jointLog] [info] iteration = 900 | max rel diff. = 0.0981588
[2019-01-15 21:42:07.518] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0765608
[2019-01-15 21:42:09.625] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0331978
[2019-01-15 21:42:11.482] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0297585
[2019-01-15 21:42:13.804] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.101034
[2019-01-15 21:42:15.948] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0168582
[2019-01-15 21:42:18.042] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0622972
[2019-01-15 21:42:19.457] [jointLog] [info] iteration = 1,574 | max rel diff. = 0.00900873
[2019-01-15 21:42:19.478] [jointLog] [info] Finished optimizer
[2019-01-15 21:42:19.478] [jointLog] [info] writing output 

[2019-01-15 21:42:20.100] [jointLog] [info] Starting Gibbs Sampler
[2019-01-15 21:43:07.003] [jointLog] [info] Finished Gibbs Sampler
