[2022-11-09 13:09:46.561] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 13:09:46.561] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 13:09:46.561] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 13:09:46.561] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 13:09:46.561] [jointLog] [info] parsing read library format
[2022-11-09 13:09:46.561] [jointLog] [info] There is 1 library.
[2022-11-09 13:09:46.561] [jointLog] [info] Loading pufferfish index
[2022-11-09 13:09:46.561] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 13:10:18.829] [jointLog] [info] done
[2022-11-09 13:10:18.878] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 13:10:19.227] [jointLog] [info] Number of decoys : 195
[2022-11-09 13:10:19.227] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 13:10:22.611] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:17:45.860] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:17:45.983] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:17:46.082] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:17:46.087] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:17:46.194] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:17:46.419] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:17:46.511] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:17:46.541] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:17:46.699] [jointLog] [info] Computed 104,825 rich equivalence classes for further processing
[2022-11-09 13:17:46.699] [jointLog] [info] Counted 3,481,435 total reads in the equivalence classes 
[2022-11-09 13:17:46.703] [jointLog] [info] Number of mappings discarded because of alignment score : 38,484,608
[2022-11-09 13:17:46.703] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,343,458
[2022-11-09 13:17:46.703] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 84,352
[2022-11-09 13:17:46.703] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,401,329
[2022-11-09 13:17:46.721] [jointLog] [warning] Only 3481435 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2022-11-09 13:17:46.721] [jointLog] [info] Mapping rate = 17.4596%

[2022-11-09 13:17:46.721] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:17:46.721] [jointLog] [info] Starting optimizer
[2022-11-09 13:17:46.804] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:17:46.817] [jointLog] [info] iteration = 0 | max rel diff. = 1820.9
[2022-11-09 13:17:46.699] [fileLog] [info] 
At end of round 0
==================
Observed 19939929 total fragments (19939929 in most recent round)

[2022-11-09 13:17:46.934] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:17:47.819] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:17:47.820] [jointLog] [info] processed bias for 0.1% of the transcripts
[2022-11-09 13:17:48.443] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:17:48.884] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:17:49.291] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:17:49.650] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 13:17:50.226] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:17:50.874] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:17:51.466] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:17:52.056] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:17:52.621] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:17:53.222] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:17:53.223] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:17:54.366] [jointLog] [info] iteration = 100 | max rel diff. = 13.5909
[2022-11-09 13:17:55.535] [jointLog] [info] iteration = 200 | max rel diff. = 5.03054
[2022-11-09 13:17:56.697] [jointLog] [info] iteration = 300 | max rel diff. = 1.37234
[2022-11-09 13:17:57.846] [jointLog] [info] iteration = 400 | max rel diff. = 0.202078
[2022-11-09 13:17:59.124] [jointLog] [info] iteration = 500 | max rel diff. = 4.8559
[2022-11-09 13:18:00.303] [jointLog] [info] iteration = 600 | max rel diff. = 1.59168
[2022-11-09 13:18:01.493] [jointLog] [info] iteration = 700 | max rel diff. = 0.0247675
[2022-11-09 13:18:02.639] [jointLog] [info] iteration = 800 | max rel diff. = 1.71052
[2022-11-09 13:18:03.817] [jointLog] [info] iteration = 900 | max rel diff. = 0.082217
[2022-11-09 13:18:05.004] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0217458
[2022-11-09 13:18:06.170] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.114024
[2022-11-09 13:18:07.534] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.409667
[2022-11-09 13:18:08.796] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0400811
[2022-11-09 13:18:09.200] [jointLog] [info] iteration = 1,336 | max rel diff. = 0.00877904
[2022-11-09 13:18:09.225] [jointLog] [info] Finished optimizer
[2022-11-09 13:18:09.225] [jointLog] [info] writing output