[2023-10-04 01:57:36.582] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 01:57:36.582] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 01:57:36.582] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 01:57:36.582] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 01:57:36.582] [jointLog] [info] parsing read library format
[2023-10-04 01:57:36.582] [jointLog] [info] There is 1 library.
[2023-10-04 01:57:36.582] [jointLog] [info] Loading pufferfish index
[2023-10-04 01:57:36.582] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 01:58:53.060] [jointLog] [info] done
[2023-10-04 01:58:53.192] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 01:59:32.391] [jointLog] [info] Number of decoys : 194
[2023-10-04 01:59:32.391] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 01:59:34.053] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 01:59:34.720] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 02:00:25.120] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-04 02:00:25.298] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-04 02:00:25.306] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-10-04 02:00:25.329] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-04 02:00:25.345] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-04 02:00:25.427] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-04 02:00:25.429] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-10-04 02:00:25.492] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-04 02:00:25.670] [jointLog] [info] Computed 88,111 rich equivalence classes for further processing
[2023-10-04 02:00:25.670] [jointLog] [info] Counted 3,727,103 total reads in the equivalence classes 
[2023-10-04 02:00:25.677] [jointLog] [info] Number of mappings discarded because of alignment score : 54,192,169
[2023-10-04 02:00:25.677] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 388,804
[2023-10-04 02:00:25.677] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 126,164
[2023-10-04 02:00:25.677] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 02:00:25.671] [fileLog] [info] 
At end of round 0
==================
Observed 4933644 total fragments (4933644 in most recent round)

[2023-10-04 02:00:27.466] [jointLog] [warning] Only 3727103 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 02:00:27.466] [jointLog] [info] Mapping rate = 75.5446%

[2023-10-04 02:00:27.466] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 02:00:27.467] [jointLog] [info] Starting optimizer
[2023-10-04 02:00:32.027] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 02:00:32.356] [jointLog] [info] iteration = 0 | max rel diff. = 78.8201
[2023-10-04 02:00:35.700] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 02:01:32.340] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 02:01:32.340] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 02:01:37.223] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 02:01:42.280] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 02:01:47.634] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 02:01:53.022] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 02:01:58.412] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 02:02:03.714] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 02:02:08.478] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 02:02:13.920] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 02:02:19.370] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 02:02:25.164] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 02:02:54.605] [jointLog] [info] iteration = 100 | max rel diff. = 11.529
[2023-10-04 02:03:25.845] [jointLog] [info] iteration = 200 | max rel diff. = 5.77908
[2023-10-04 02:03:57.129] [jointLog] [info] iteration = 300 | max rel diff. = 0.402932
[2023-10-04 02:04:29.192] [jointLog] [info] iteration = 400 | max rel diff. = 0.136653
[2023-10-04 02:05:00.737] [jointLog] [info] iteration = 500 | max rel diff. = 0.0332673
[2023-10-04 02:05:32.606] [jointLog] [info] iteration = 600 | max rel diff. = 0.123196
[2023-10-04 02:06:04.602] [jointLog] [info] iteration = 700 | max rel diff. = 0.0460105
[2023-10-04 02:06:11.912] [jointLog] [info] iteration = 724 | max rel diff. = 0.00960585
[2023-10-04 02:06:13.902] [jointLog] [info] Finished optimizer
[2023-10-04 02:06:13.902] [jointLog] [info] writing output