[2023-09-24 07:25:15.384] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 07:25:15.384] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 07:25:15.384] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 07:25:15.384] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 07:25:15.384] [jointLog] [info] parsing read library format
[2023-09-24 07:25:15.384] [jointLog] [info] There is 1 library.
[2023-09-24 07:25:15.384] [jointLog] [info] Loading pufferfish index
[2023-09-24 07:25:15.384] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 07:26:36.186] [jointLog] [info] done
[2023-09-24 07:26:36.343] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 07:27:17.572] [jointLog] [info] Number of decoys : 194
[2023-09-24 07:27:17.572] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 07:27:19.518] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 07:27:20.717] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 07:27:54.414] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-24 07:27:54.463] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-24 07:27:54.504] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-24 07:27:54.601] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-24 07:27:54.673] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2023-09-24 07:27:54.819] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-24 07:27:54.876] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-24 07:27:54.884] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-09-24 07:27:55.079] [jointLog] [info] Computed 71,400 rich equivalence classes for further processing
[2023-09-24 07:27:55.079] [jointLog] [info] Counted 1,976,282 total reads in the equivalence classes 
[2023-09-24 07:27:55.087] [jointLog] [info] Number of mappings discarded because of alignment score : 42,799,804
[2023-09-24 07:27:55.087] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 262,889
[2023-09-24 07:27:55.087] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 66,213
[2023-09-24 07:27:55.087] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 07:27:55.080] [fileLog] [info] 
At end of round 0
==================
Observed 2610888 total fragments (2610888 in most recent round)

[2023-09-24 07:27:56.178] [jointLog] [warning] Only 1976282 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 07:27:56.178] [jointLog] [info] Mapping rate = 75.6939%

[2023-09-24 07:27:56.178] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 07:27:56.178] [jointLog] [info] Starting optimizer
[2023-09-24 07:28:00.581] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 07:28:00.917] [jointLog] [info] iteration = 0 | max rel diff. = 40.5399
[2023-09-24 07:28:04.351] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 07:28:51.211] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 07:28:51.212] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 07:28:55.561] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 07:28:59.689] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 07:29:04.155] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 07:29:08.392] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 07:29:13.018] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 07:29:17.357] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 07:29:21.619] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 07:29:26.003] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 07:29:30.234] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 07:29:34.634] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 07:30:06.198] [jointLog] [info] iteration = 100 | max rel diff. = 15.4695
[2023-09-24 07:30:39.387] [jointLog] [info] iteration = 200 | max rel diff. = 0.958311
[2023-09-24 07:31:12.086] [jointLog] [info] iteration = 300 | max rel diff. = 11.5166
[2023-09-24 07:31:45.108] [jointLog] [info] iteration = 400 | max rel diff. = 0.0972696
[2023-09-24 07:32:18.181] [jointLog] [info] iteration = 500 | max rel diff. = 0.0566034
[2023-09-24 07:32:51.075] [jointLog] [info] iteration = 600 | max rel diff. = 0.0682814
[2023-09-24 07:33:23.900] [jointLog] [info] iteration = 700 | max rel diff. = 0.0225063
[2023-09-24 07:33:57.131] [jointLog] [info] iteration = 800 | max rel diff. = 0.0487424
[2023-09-24 07:34:30.262] [jointLog] [info] iteration = 900 | max rel diff. = 0.142301
[2023-09-24 07:35:03.350] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.189639
[2023-09-24 07:35:24.432] [jointLog] [info] iteration = 1,064 | max rel diff. = 0.0014558
[2023-09-24 07:35:26.617] [jointLog] [info] Finished optimizer
[2023-09-24 07:35:26.617] [jointLog] [info] writing output