[2019-01-30 21:10:25.436] [jointLog] [info] parsing read library format
[2019-01-30 21:10:25.436] [jointLog] [info] There is 1 library.
[2019-01-30 21:10:25.497] [jointLog] [info] Loading Quasi index
[2019-01-30 21:10:25.497] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:10:25.896] [jointLog] [info] done
[2019-01-30 21:10:25.896] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:11:10.326] [jointLog] [info] Computed 7296 rich equivalence classes for further processing
[2019-01-30 21:11:10.326] [jointLog] [info] Counted 1550851 total reads in the equivalence classes 
[2019-01-30 21:11:10.337] [jointLog] [warning] 0.0114771% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-01-30 21:11:10.338] [jointLog] [warning] Only 1550851 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:11:10.338] [jointLog] [info] Mapping rate = 8.4437%

[2019-01-30 21:11:10.338] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:11:10.338] [jointLog] [info] Starting optimizer
[2019-01-30 21:11:10.343] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:11:10.343] [jointLog] [info] iteration = 0 | max rel diff. = 415.306
[2019-01-30 21:11:10.362] [jointLog] [info] iteration = 100 | max rel diff. = 0.123525
[2019-01-30 21:11:10.378] [jointLog] [info] iteration = 200 | max rel diff. = 0.0531477
[2019-01-30 21:11:10.395] [jointLog] [info] iteration = 300 | max rel diff. = 0.03914
[2019-01-30 21:11:10.412] [jointLog] [info] iteration = 400 | max rel diff. = 0.0282139
[2019-01-30 21:11:10.430] [jointLog] [info] iteration = 500 | max rel diff. = 0.0208173
[2019-01-30 21:11:10.447] [jointLog] [info] iteration = 600 | max rel diff. = 0.0169571
[2019-01-30 21:11:10.327] [fileLog] [info] 
At end of round 0
==================
Observed 18366968 total fragments (18366968 in most recent round)

[2019-01-30 21:11:10.465] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151659
[2019-01-30 21:11:10.482] [jointLog] [info] iteration = 800 | max rel diff. = 0.0115065
[2019-01-30 21:11:10.499] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113234
[2019-01-30 21:11:10.515] [jointLog] [info] iteration = 987 | max rel diff. = 0.00953055
[2019-01-30 21:11:10.515] [jointLog] [info] Finished optimizer
[2019-01-30 21:11:10.515] [jointLog] [info] writing output 

[2019-01-30 21:11:10.526] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_02/lib_format_counts.json for details