[2023-09-15 18:24:35.068] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-15 18:24:35.068] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-15 18:24:35.068] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-15 18:24:35.068] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-15 18:24:35.068] [jointLog] [info] parsing read library format
[2023-09-15 18:24:35.068] [jointLog] [info] There is 1 library.
[2023-09-15 18:24:35.068] [jointLog] [info] Loading pufferfish index
[2023-09-15 18:24:35.068] [jointLog] [info] Loading dense pufferfish index.
[2023-09-15 18:25:56.496] [jointLog] [info] done
[2023-09-15 18:25:56.634] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-15 18:26:32.388] [jointLog] [info] Number of decoys : 194
[2023-09-15 18:26:32.388] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-15 18:26:33.962] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-15 18:26:35.097] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-15 18:27:12.007] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-15 18:27:12.021] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-09-15 18:27:12.083] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-15 18:27:12.102] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-15 18:27:12.137] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-15 18:27:12.169] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-09-15 18:27:12.207] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-09-15 18:27:12.286] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-15 18:27:12.545] [fileLog] [info] 
At end of round 0
==================
Observed 5112400 total fragments (5112400 in most recent round)

[2023-09-15 18:27:12.544] [jointLog] [info] Computed 162,501 rich equivalence classes for further processing
[2023-09-15 18:27:12.544] [jointLog] [info] Counted 4,696,229 total reads in the equivalence classes 
[2023-09-15 18:27:12.554] [jointLog] [info] Number of mappings discarded because of alignment score : 8,523,296
[2023-09-15 18:27:12.554] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 91,480
[2023-09-15 18:27:12.554] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 50,089
[2023-09-15 18:27:12.554] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-15 18:27:13.704] [jointLog] [warning] Only 4696229 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-15 18:27:13.704] [jointLog] [info] Mapping rate = 91.8596%

[2023-09-15 18:27:13.704] [jointLog] [info] finished quantifyLibrary()
[2023-09-15 18:27:13.704] [jointLog] [info] Starting optimizer
[2023-09-15 18:27:17.540] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-15 18:27:17.872] [jointLog] [info] iteration = 0 | max rel diff. = 91.5571
[2023-09-15 18:27:21.292] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-15 18:28:31.979] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-15 18:28:31.979] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-15 18:28:38.620] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-15 18:28:45.802] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-15 18:28:52.151] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-15 18:28:58.911] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-15 18:29:04.968] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-15 18:29:11.413] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-15 18:29:17.873] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-15 18:29:24.088] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-15 18:29:30.814] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-15 18:29:37.291] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-15 18:29:37.300] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-15 18:30:07.157] [jointLog] [info] iteration = 100 | max rel diff. = 9.7953
[2023-09-15 18:30:40.070] [jointLog] [info] iteration = 200 | max rel diff. = 9.98195
[2023-09-15 18:31:11.971] [jointLog] [info] iteration = 300 | max rel diff. = 2.37935
[2023-09-15 18:31:43.626] [jointLog] [info] iteration = 400 | max rel diff. = 1.44453
[2023-09-15 18:32:15.464] [jointLog] [info] iteration = 500 | max rel diff. = 10.958
[2023-09-15 18:32:47.167] [jointLog] [info] iteration = 600 | max rel diff. = 0.180102
[2023-09-15 18:33:18.810] [jointLog] [info] iteration = 700 | max rel diff. = 0.30905
[2023-09-15 18:33:50.754] [jointLog] [info] iteration = 800 | max rel diff. = 0.0455613
[2023-09-15 18:34:27.444] [jointLog] [info] iteration = 900 | max rel diff. = 0.129859
[2023-09-15 18:35:04.504] [jointLog] [info] iteration = 1,000 | max rel diff. = 5.45345
[2023-09-15 18:35:39.503] [jointLog] [info] iteration = 1,096 | max rel diff. = 0.00811512
[2023-09-15 18:35:41.850] [jointLog] [info] Finished optimizer
[2023-09-15 18:35:41.850] [jointLog] [info] writing output