[2019-01-30 21:15:57.648] [jointLog] [info] parsing read library format
[2019-01-30 21:15:57.648] [jointLog] [info] There is 1 library.
[2019-01-30 21:15:57.710] [jointLog] [info] Loading Quasi index
[2019-01-30 21:15:57.710] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:15:58.095] [jointLog] [info] done
[2019-01-30 21:15:58.095] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:16:51.711] [jointLog] [info] Computed 7631 rich equivalence classes for further processing
[2019-01-30 21:16:51.711] [jointLog] [info] Counted 2077905 total reads in the equivalence classes 
[2019-01-30 21:16:51.722] [jointLog] [warning] 0.0142576% 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 21:16:51.723] [jointLog] [warning] Only 2077905 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 21:16:51.723] [jointLog] [info] Mapping rate = 9.47121%

[2019-01-30 21:16:51.723] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:16:51.723] [jointLog] [info] Starting optimizer
[2019-01-30 21:16:51.728] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:16:51.728] [jointLog] [info] iteration = 0 | max rel diff. = 467.258
[2019-01-30 21:16:51.746] [jointLog] [info] iteration = 100 | max rel diff. = 0.12376
[2019-01-30 21:16:51.763] [jointLog] [info] iteration = 200 | max rel diff. = 0.0600567
[2019-01-30 21:16:51.780] [jointLog] [info] iteration = 300 | max rel diff. = 0.0368969
[2019-01-30 21:16:51.796] [jointLog] [info] iteration = 400 | max rel diff. = 0.0285312
[2019-01-30 21:16:51.811] [jointLog] [info] iteration = 500 | max rel diff. = 0.0204312
[2019-01-30 21:16:51.827] [jointLog] [info] iteration = 600 | max rel diff. = 0.0203213
[2019-01-30 21:16:51.842] [jointLog] [info] iteration = 700 | max rel diff. = 0.0156616
[2019-01-30 21:16:51.857] [jointLog] [info] iteration = 800 | max rel diff. = 0.0123596
[2019-01-30 21:16:51.872] [jointLog] [info] iteration = 900 | max rel diff. = 0.0116243
[2019-01-30 21:16:51.890] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116244
[2019-01-30 21:16:51.712] [fileLog] [info] 
At end of round 0
==================
Observed 21939168 total fragments (21939168 in most recent round)

[2019-01-30 21:16:51.892] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00897672
[2019-01-30 21:16:51.893] [jointLog] [info] Finished optimizer
[2019-01-30 21:16:51.893] [jointLog] [info] writing output 

[2019-01-30 21:16:51.904] [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_44_02/lib_format_counts.json for details