[2019-01-30 21:23:53.517] [jointLog] [info] parsing read library format
[2019-01-30 21:23:53.517] [jointLog] [info] There is 1 library.
[2019-01-30 21:23:53.579] [jointLog] [info] Loading Quasi index
[2019-01-30 21:23:53.579] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:23:53.990] [jointLog] [info] done
[2019-01-30 21:23:53.990] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:24:58.227] [jointLog] [info] Computed 7721 rich equivalence classes for further processing
[2019-01-30 21:24:58.227] [jointLog] [info] Counted 2334407 total reads in the equivalence classes 
[2019-01-30 21:24:58.238] [jointLog] [warning] 0.0152392% 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 21:24:58.238] [jointLog] [warning] Only 2334407 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 21:24:58.238] [jointLog] [info] Mapping rate = 8.82085%

[2019-01-30 21:24:58.238] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:24:58.239] [jointLog] [info] Starting optimizer
[2019-01-30 21:24:58.244] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:24:58.244] [jointLog] [info] iteration = 0 | max rel diff. = 595.466
[2019-01-30 21:24:58.262] [jointLog] [info] iteration = 100 | max rel diff. = 0.123189
[2019-01-30 21:24:58.278] [jointLog] [info] iteration = 200 | max rel diff. = 0.055328
[2019-01-30 21:24:58.295] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417837
[2019-01-30 21:24:58.311] [jointLog] [info] iteration = 400 | max rel diff. = 0.0269787
[2019-01-30 21:24:58.327] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220706
[2019-01-30 21:24:58.342] [jointLog] [info] iteration = 600 | max rel diff. = 0.0194603
[2019-01-30 21:24:58.227] [fileLog] [info] 
At end of round 0
==================
Observed 26464646 total fragments (26464646 in most recent round)

[2019-01-30 21:24:58.357] [jointLog] [info] iteration = 700 | max rel diff. = 0.0201996
[2019-01-30 21:24:58.373] [jointLog] [info] iteration = 800 | max rel diff. = 0.0124207
[2019-01-30 21:24:58.390] [jointLog] [info] iteration = 900 | max rel diff. = 0.0124209
[2019-01-30 21:24:58.406] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0102374
[2019-01-30 21:24:58.412] [jointLog] [info] iteration = 1034 | max rel diff. = 0.00882132
[2019-01-30 21:24:58.412] [jointLog] [info] Finished optimizer
[2019-01-30 21:24:58.412] [jointLog] [info] writing output 

[2019-01-30 21:24:58.423] [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: non-bleached_44_03/lib_format_counts.json for details