[2023-09-27 19:08:22.154] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-27 19:08:22.154] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-27 19:08:22.154] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-27 19:08:22.154] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-27 19:08:22.154] [jointLog] [info] parsing read library format
[2023-09-27 19:08:22.154] [jointLog] [info] There is 1 library.
[2023-09-27 19:08:22.154] [jointLog] [info] Loading pufferfish index
[2023-09-27 19:08:22.154] [jointLog] [info] Loading dense pufferfish index.
[2023-09-27 19:09:40.073] [jointLog] [info] done
[2023-09-27 19:09:40.199] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-27 19:10:16.518] [jointLog] [info] Number of decoys : 194
[2023-09-27 19:10:16.518] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-27 19:10:18.150] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-27 19:10:19.022] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-27 19:10:53.716] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-09-27 19:10:53.730] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2023-09-27 19:10:53.788] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-09-27 19:10:53.836] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2023-09-27 19:10:53.843] [jointLog] [info] Thread saw mini-batch with a maximum of 2.68% zero probability fragments
[2023-09-27 19:10:53.982] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-09-27 19:10:54.002] [jointLog] [info] Thread saw mini-batch with a maximum of 2.68% zero probability fragments
[2023-09-27 19:10:54.046] [jointLog] [info] Thread saw mini-batch with a maximum of 2.50% zero probability fragments
[2023-09-27 19:10:54.200] [jointLog] [info] Computed 85,768 rich equivalence classes for further processing
[2023-09-27 19:10:54.200] [jointLog] [info] Counted 2,199,884 total reads in the equivalence classes 
[2023-09-27 19:10:54.208] [jointLog] [info] Number of mappings discarded because of alignment score : 34,018,384
[2023-09-27 19:10:54.208] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 185,260
[2023-09-27 19:10:54.208] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 47,726
[2023-09-27 19:10:54.208] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-27 19:10:54.201] [fileLog] [info] 
At end of round 0
==================
Observed 2951431 total fragments (2951431 in most recent round)

[2023-09-27 19:10:55.151] [jointLog] [warning] Only 2199884 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-27 19:10:55.151] [jointLog] [info] Mapping rate = 74.5362%

[2023-09-27 19:10:55.151] [jointLog] [info] finished quantifyLibrary()
[2023-09-27 19:10:55.152] [jointLog] [info] Starting optimizer
[2023-09-27 19:10:59.213] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-27 19:10:59.543] [jointLog] [info] iteration = 0 | max rel diff. = 43.8849
[2023-09-27 19:11:02.830] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-27 19:11:54.034] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-27 19:11:54.035] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-27 19:11:58.561] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-27 19:12:03.062] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-27 19:12:07.900] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-27 19:12:12.742] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-27 19:12:17.424] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-27 19:12:22.083] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-27 19:12:26.729] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-27 19:12:31.243] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-27 19:12:35.703] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-27 19:12:40.250] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-27 19:12:40.250] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-27 19:13:10.362] [jointLog] [info] iteration = 100 | max rel diff. = 16.7208
[2023-09-27 19:13:43.019] [jointLog] [info] iteration = 200 | max rel diff. = 7.21762
[2023-09-27 19:14:19.532] [jointLog] [info] iteration = 300 | max rel diff. = 0.253555
[2023-09-27 19:14:57.734] [jointLog] [info] iteration = 400 | max rel diff. = 0.119056
[2023-09-27 19:15:33.138] [jointLog] [info] iteration = 500 | max rel diff. = 0.268363
[2023-09-27 19:16:07.545] [jointLog] [info] iteration = 600 | max rel diff. = 0.0600285
[2023-09-27 19:16:43.033] [jointLog] [info] iteration = 700 | max rel diff. = 0.0226184
[2023-09-27 19:17:18.514] [jointLog] [info] iteration = 800 | max rel diff. = 0.0956466
[2023-09-27 19:17:41.405] [jointLog] [info] iteration = 867 | max rel diff. = 0.0084851
[2023-09-27 19:17:43.617] [jointLog] [info] Finished optimizer
[2023-09-27 19:17:43.617] [jointLog] [info] writing output