[2023-08-26 04:11:47.166] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-26 04:11:47.166] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-26 04:11:47.166] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-26 04:11:47.166] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-26 04:11:47.166] [jointLog] [info] parsing read library format
[2023-08-26 04:11:47.166] [jointLog] [info] There is 1 library.
[2023-08-26 04:11:47.166] [jointLog] [info] Loading pufferfish index
[2023-08-26 04:11:47.167] [jointLog] [info] Loading dense pufferfish index.
[2023-08-26 04:13:02.096] [jointLog] [info] done
[2023-08-26 04:13:02.278] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-26 04:13:43.862] [jointLog] [info] Number of decoys : 194
[2023-08-26 04:13:43.862] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-26 04:13:49.257] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-26 04:22:07.263] [jointLog] [info] Thread saw mini-batch with a maximum of 12.46% zero probability fragments
[2023-08-26 04:22:07.314] [jointLog] [info] Thread saw mini-batch with a maximum of 12.12% zero probability fragments
[2023-08-26 04:22:07.548] [jointLog] [info] Thread saw mini-batch with a maximum of 12.14% zero probability fragments
[2023-08-26 04:22:07.677] [jointLog] [info] Thread saw mini-batch with a maximum of 12.24% zero probability fragments
[2023-08-26 04:22:07.677] [jointLog] [info] Thread saw mini-batch with a maximum of 12.06% zero probability fragments
[2023-08-26 04:22:07.692] [jointLog] [info] Thread saw mini-batch with a maximum of 12.04% zero probability fragments
[2023-08-26 04:22:07.710] [jointLog] [info] Thread saw mini-batch with a maximum of 12.26% zero probability fragments
[2023-08-26 04:22:07.751] [jointLog] [info] Thread saw mini-batch with a maximum of 12.20% zero probability fragments
[2023-08-26 04:22:08.366] [jointLog] [info] Computed 434,414 rich equivalence classes for further processing
[2023-08-26 04:22:08.366] [jointLog] [info] Counted 20,346,368 total reads in the equivalence classes 
[2023-08-26 04:22:08.377] [jointLog] [info] Number of mappings discarded because of alignment score : 19,315,881
[2023-08-26 04:22:08.377] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,916,490
[2023-08-26 04:22:08.377] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 918,528
[2023-08-26 04:22:08.377] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,941,896
[2023-08-26 04:22:08.377] [jointLog] [info] Mapping rate = 78.9907%

[2023-08-26 04:22:08.377] [jointLog] [info] finished quantifyLibrary()
[2023-08-26 04:22:08.378] [jointLog] [info] Starting optimizer
[2023-08-26 04:22:08.367] [fileLog] [info] 
At end of round 0
==================
Observed 25757927 total fragments (25757927 in most recent round)

[2023-08-26 04:22:14.337] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-26 04:22:14.711] [jointLog] [info] iteration = 0 | max rel diff. = 294.549
[2023-08-26 04:22:18.363] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-26 04:26:35.976] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-26 04:26:35.977] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-26 04:26:57.117] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-26 04:27:18.709] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-26 04:27:40.017] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-26 04:28:01.834] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-26 04:28:22.784] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-26 04:28:43.261] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-26 04:29:05.397] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-26 04:29:26.577] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-26 04:29:47.675] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-26 04:30:08.541] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-26 04:30:42.017] [jointLog] [info] iteration = 100 | max rel diff. = 14.8464
[2023-08-26 04:31:18.974] [jointLog] [info] iteration = 200 | max rel diff. = 9.44171
[2023-08-26 04:31:55.575] [jointLog] [info] iteration = 300 | max rel diff. = 18.8564
[2023-08-26 04:32:31.799] [jointLog] [info] iteration = 400 | max rel diff. = 0.628532
[2023-08-26 04:33:07.951] [jointLog] [info] iteration = 500 | max rel diff. = 0.67547
[2023-08-26 04:33:44.267] [jointLog] [info] iteration = 600 | max rel diff. = 0.229101
[2023-08-26 04:34:20.066] [jointLog] [info] iteration = 700 | max rel diff. = 5.23809
[2023-08-26 04:34:55.796] [jointLog] [info] iteration = 800 | max rel diff. = 0.380042
[2023-08-26 04:35:31.742] [jointLog] [info] iteration = 900 | max rel diff. = 0.062951
[2023-08-26 04:36:07.499] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.460117
[2023-08-26 04:36:42.550] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.470125
[2023-08-26 04:37:17.754] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0952083
[2023-08-26 04:37:31.044] [jointLog] [info] iteration = 1,239 | max rel diff. = 0.00868247
[2023-08-26 04:37:33.359] [jointLog] [info] Finished optimizer
[2023-08-26 04:37:33.359] [jointLog] [info] writing output