[2022-11-09 12:54:44.412] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 12:54:44.412] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 12:54:44.412] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 12:54:44.412] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 12:54:44.412] [jointLog] [info] parsing read library format
[2022-11-09 12:54:44.412] [jointLog] [info] There is 1 library.
[2022-11-09 12:54:44.412] [jointLog] [info] Loading pufferfish index
[2022-11-09 12:54:44.412] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 12:55:16.119] [jointLog] [info] done
[2022-11-09 12:55:16.168] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 12:55:16.709] [jointLog] [info] Number of decoys : 195
[2022-11-09 12:55:16.709] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 12:55:20.213] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:01:57.454] [jointLog] [info] Thread saw mini-batch with a maximum of 0.25% zero probability fragments
[2022-11-09 13:01:57.504] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:57.572] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 13:01:57.620] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:57.735] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:01:57.774] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:57.774] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:58.031] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:01:58.183] [jointLog] [info] Computed 102,036 rich equivalence classes for further processing
[2022-11-09 13:01:58.183] [jointLog] [info] Counted 3,056,942 total reads in the equivalence classes 
[2022-11-09 13:01:58.185] [jointLog] [info] Number of mappings discarded because of alignment score : 36,028,797
[2022-11-09 13:01:58.185] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,111,420
[2022-11-09 13:01:58.185] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 58,820
[2022-11-09 13:01:58.185] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,575,057
[2022-11-09 13:01:58.183] [fileLog] [info] 
At end of round 0
==================
Observed 18915393 total fragments (18915393 in most recent round)

[2022-11-09 13:01:58.202] [jointLog] [warning] Only 3056942 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 13:01:58.202] [jointLog] [info] Mapping rate = 16.1611%

[2022-11-09 13:01:58.202] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:01:58.211] [jointLog] [info] Starting optimizer
[2022-11-09 13:01:58.289] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:01:58.304] [jointLog] [info] iteration = 0 | max rel diff. = 1582.59
[2022-11-09 13:01:58.401] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:01:58.987] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:01:58.987] [jointLog] [info] processed bias for 0.2% of the transcripts
[2022-11-09 13:01:59.362] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:01:59.769] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:02:00.102] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:02:00.399] [jointLog] [info] processed bias for 40.1% of the transcripts
[2022-11-09 13:02:00.615] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:02:00.834] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:02:01.203] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:02:01.550] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:02:01.914] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:02:02.258] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:02:02.258] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:02:03.206] [jointLog] [info] iteration = 100 | max rel diff. = 8.35031
[2022-11-09 13:02:04.345] [jointLog] [info] iteration = 200 | max rel diff. = 3.54489
[2022-11-09 13:02:05.616] [jointLog] [info] iteration = 300 | max rel diff. = 2.54934
[2022-11-09 13:02:06.902] [jointLog] [info] iteration = 400 | max rel diff. = 0.227646
[2022-11-09 13:02:07.963] [jointLog] [info] iteration = 500 | max rel diff. = 3.11561
[2022-11-09 13:02:09.058] [jointLog] [info] iteration = 600 | max rel diff. = 0.894703
[2022-11-09 13:02:10.196] [jointLog] [info] iteration = 700 | max rel diff. = 1.58648
[2022-11-09 13:02:11.299] [jointLog] [info] iteration = 800 | max rel diff. = 0.0189707
[2022-11-09 13:02:12.458] [jointLog] [info] iteration = 900 | max rel diff. = 0.0486763
[2022-11-09 13:02:13.653] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0352807
[2022-11-09 13:02:14.828] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.110562
[2022-11-09 13:02:16.019] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.115262
[2022-11-09 13:02:17.111] [jointLog] [info] iteration = 1,300 | max rel diff. = 16.5382
[2022-11-09 13:02:18.171] [jointLog] [info] iteration = 1,396 | max rel diff. = 0.00305824
[2022-11-09 13:02:18.193] [jointLog] [info] Finished optimizer
[2022-11-09 13:02:18.193] [jointLog] [info] writing output