[2022-11-09 13:02:22.175] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 13:02:22.175] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 13:02:22.175] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 13:02:22.175] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 13:02:22.175] [jointLog] [info] parsing read library format
[2022-11-09 13:02:22.175] [jointLog] [info] There is 1 library.
[2022-11-09 13:02:22.175] [jointLog] [info] Loading pufferfish index
[2022-11-09 13:02:22.175] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 13:02:43.009] [jointLog] [info] done
[2022-11-09 13:02:43.058] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 13:02:43.581] [jointLog] [info] Number of decoys : 195
[2022-11-09 13:02:43.581] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 13:02:47.013] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 13:09:39.884] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:39.903] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:39.919] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:39.982] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:40.218] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:40.233] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:40.275] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 13:09:40.311] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 13:09:40.447] [jointLog] [info] Computed 101,907 rich equivalence classes for further processing
[2022-11-09 13:09:40.447] [jointLog] [info] Counted 2,925,909 total reads in the equivalence classes 
[2022-11-09 13:09:40.448] [fileLog] [info] 
At end of round 0
==================
Observed 20020409 total fragments (20020409 in most recent round)

[2022-11-09 13:09:40.450] [jointLog] [info] Number of mappings discarded because of alignment score : 38,644,552
[2022-11-09 13:09:40.450] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,284,047
[2022-11-09 13:09:40.450] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 56,597
[2022-11-09 13:09:40.450] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,802,120
[2022-11-09 13:09:40.467] [jointLog] [warning] Only 2925909 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2022-11-09 13:09:40.467] [jointLog] [info] Mapping rate = 14.6146%

[2022-11-09 13:09:40.467] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 13:09:40.467] [jointLog] [info] Starting optimizer
[2022-11-09 13:09:40.537] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 13:09:40.550] [jointLog] [info] iteration = 0 | max rel diff. = 1537.25
[2022-11-09 13:09:40.650] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 13:09:41.186] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 13:09:41.187] [jointLog] [info] processed bias for 0.2% of the transcripts
[2022-11-09 13:09:41.539] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 13:09:41.875] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 13:09:42.157] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 13:09:42.446] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 13:09:42.672] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 13:09:42.850] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 13:09:43.103] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 13:09:43.404] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 13:09:43.751] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 13:09:44.113] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 13:09:45.253] [jointLog] [info] iteration = 100 | max rel diff. = 20.561
[2022-11-09 13:09:46.355] [jointLog] [info] iteration = 200 | max rel diff. = 3.82112
[2022-11-09 13:09:47.462] [jointLog] [info] iteration = 300 | max rel diff. = 1.40612
[2022-11-09 13:09:48.624] [jointLog] [info] iteration = 400 | max rel diff. = 3.61291
[2022-11-09 13:09:49.777] [jointLog] [info] iteration = 500 | max rel diff. = 0.954042
[2022-11-09 13:09:50.934] [jointLog] [info] iteration = 600 | max rel diff. = 0.527581
[2022-11-09 13:09:52.066] [jointLog] [info] iteration = 700 | max rel diff. = 0.040325
[2022-11-09 13:09:52.838] [jointLog] [info] iteration = 769 | max rel diff. = 0.00928407
[2022-11-09 13:09:52.859] [jointLog] [info] Finished optimizer
[2022-11-09 13:09:52.859] [jointLog] [info] writing output