[2023-10-03 07:38:29.947] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 07:38:29.947] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 07:38:29.947] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 07:38:29.947] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 07:38:29.947] [jointLog] [info] parsing read library format
[2023-10-03 07:38:29.947] [jointLog] [info] There is 1 library.
[2023-10-03 07:38:29.948] [jointLog] [info] Loading pufferfish index
[2023-10-03 07:38:29.948] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 07:40:00.433] [jointLog] [info] done
[2023-10-03 07:40:00.642] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 07:40:43.335] [jointLog] [info] Number of decoys : 194
[2023-10-03 07:40:43.336] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 07:40:45.335] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 07:40:46.806] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 07:41:37.199] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-03 07:41:37.313] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-10-03 07:41:37.529] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-03 07:41:37.537] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2023-10-03 07:41:37.573] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-03 07:41:37.590] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-03 07:41:37.921] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-03 07:41:38.000] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2023-10-03 07:41:38.258] [jointLog] [info] Computed 81,093 rich equivalence classes for further processing
[2023-10-03 07:41:38.258] [jointLog] [info] Counted 2,057,073 total reads in the equivalence classes 
[2023-10-03 07:41:38.268] [jointLog] [info] Number of mappings discarded because of alignment score : 45,369,507
[2023-10-03 07:41:38.268] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 265,697
[2023-10-03 07:41:38.268] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 59,571
[2023-10-03 07:41:38.268] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 07:41:38.259] [fileLog] [info] 
At end of round 0
==================
Observed 2702791 total fragments (2702791 in most recent round)

[2023-10-03 07:41:39.251] [jointLog] [warning] Only 2057073 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 07:41:39.251] [jointLog] [info] Mapping rate = 76.1092%

[2023-10-03 07:41:39.251] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 07:41:39.251] [jointLog] [info] Starting optimizer
[2023-10-03 07:41:43.929] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 07:41:44.300] [jointLog] [info] iteration = 0 | max rel diff. = 38.3389
[2023-10-03 07:41:47.940] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 07:42:44.397] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 07:42:44.398] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 07:42:49.574] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 07:42:55.028] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 07:43:00.140] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 07:43:05.181] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 07:43:10.517] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 07:43:15.796] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 07:43:21.184] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 07:43:26.472] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 07:43:32.031] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 07:43:37.368] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 07:44:08.477] [jointLog] [info] iteration = 100 | max rel diff. = 7.30969
[2023-10-03 07:44:43.726] [jointLog] [info] iteration = 200 | max rel diff. = 1.63841
[2023-10-03 07:45:18.850] [jointLog] [info] iteration = 300 | max rel diff. = 0.177752
[2023-10-03 07:45:54.382] [jointLog] [info] iteration = 400 | max rel diff. = 16.9055
[2023-10-03 07:46:30.634] [jointLog] [info] iteration = 500 | max rel diff. = 0.0324274
[2023-10-03 07:47:06.914] [jointLog] [info] iteration = 600 | max rel diff. = 0.118207
[2023-10-03 07:47:18.911] [jointLog] [info] iteration = 635 | max rel diff. = 0.00631709
[2023-10-03 07:47:20.850] [jointLog] [info] Finished optimizer
[2023-10-03 07:47:20.850] [jointLog] [info] writing output