[2023-09-29 09:26:17.855] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-29 09:26:17.855] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-29 09:26:17.855] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-29 09:26:17.855] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-29 09:26:17.855] [jointLog] [info] parsing read library format
[2023-09-29 09:26:17.855] [jointLog] [info] There is 1 library.
[2023-09-29 09:26:17.855] [jointLog] [info] Loading pufferfish index
[2023-09-29 09:26:17.855] [jointLog] [info] Loading dense pufferfish index.
[2023-09-29 09:27:28.748] [jointLog] [info] done
[2023-09-29 09:27:28.870] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-29 09:28:03.079] [jointLog] [info] Number of decoys : 194
[2023-09-29 09:28:03.079] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-29 09:28:04.274] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-29 09:28:05.547] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-29 09:28:21.064] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-29 09:28:21.088] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-29 09:28:21.100] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-09-29 09:28:21.147] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-29 09:28:21.247] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-29 09:28:21.314] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-29 09:28:21.321] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-29 09:28:21.514] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-09-29 09:28:21.633] [jointLog] [info] Computed 61,625 rich equivalence classes for further processing
[2023-09-29 09:28:21.633] [jointLog] [info] Counted 829,844 total reads in the equivalence classes 
[2023-09-29 09:28:21.640] [jointLog] [info] Number of mappings discarded because of alignment score : 16,204,094
[2023-09-29 09:28:21.640] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 91,136
[2023-09-29 09:28:21.640] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 26,821
[2023-09-29 09:28:21.640] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-29 09:28:21.634] [fileLog] [info] 
At end of round 0
==================
Observed 1092986 total fragments (1092986 in most recent round)

[2023-09-29 09:28:22.472] [jointLog] [warning] Only 829844 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-29 09:28:22.472] [jointLog] [info] Mapping rate = 75.9245%

[2023-09-29 09:28:22.472] [jointLog] [info] finished quantifyLibrary()
[2023-09-29 09:28:22.472] [jointLog] [info] Starting optimizer
[2023-09-29 09:28:25.896] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-29 09:28:26.218] [jointLog] [info] iteration = 0 | max rel diff. = 15.3493
[2023-09-29 09:28:29.423] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-29 09:29:17.700] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-29 09:29:17.700] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-29 09:29:21.932] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-29 09:29:26.403] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-29 09:29:31.185] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-29 09:29:35.627] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-29 09:29:39.848] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-29 09:29:44.377] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-29 09:29:49.033] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-29 09:29:53.493] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-29 09:29:57.716] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-29 09:30:02.401] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-29 09:30:32.393] [jointLog] [info] iteration = 100 | max rel diff. = 8.91989
[2023-09-29 09:31:04.926] [jointLog] [info] iteration = 200 | max rel diff. = 0.102297
[2023-09-29 09:31:37.644] [jointLog] [info] iteration = 300 | max rel diff. = 0.0894316
[2023-09-29 09:32:10.223] [jointLog] [info] iteration = 400 | max rel diff. = 0.0237043
[2023-09-29 09:32:26.166] [jointLog] [info] iteration = 449 | max rel diff. = 0.0036341
[2023-09-29 09:32:28.334] [jointLog] [info] Finished optimizer
[2023-09-29 09:32:28.334] [jointLog] [info] writing output