[2020-04-26 11:00:22.242] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 11:00:22.242] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 11:00:22.242] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 11:00:22.242] [jointLog] [info] parsing read library format
[2020-04-26 11:00:22.242] [jointLog] [info] There is 1 library.
[2020-04-26 11:00:22.308] [jointLog] [info] Loading pufferfish index
[2020-04-26 11:00:22.308] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 11:00:22.469] [jointLog] [info] done
[2020-04-26 11:00:22.469] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 11:00:22.482] [jointLog] [info] Number of decoys : 0
[2020-04-26 11:00:24.121] [jointLog] [info] Computed 4,768 rich equivalence classes for further processing
[2020-04-26 11:00:24.121] [jointLog] [info] Counted 26,916 total reads in the equivalence classes 
[2020-04-26 11:00:24.163] [jointLog] [info] Number of mappings discarded because of alignment score : 21,743
[2020-04-26 11:00:24.163] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,769
[2020-04-26 11:00:24.163] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 11:00:24.163] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 79
[2020-04-26 11:00:24.167] [jointLog] [warning] Only 26916 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-26 11:00:24.167] [jointLog] [info] Mapping rate = 89.1878%

[2020-04-26 11:00:24.167] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 11:00:24.169] [jointLog] [info] Starting optimizer
[2020-04-26 11:00:24.180] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 11:00:24.183] [jointLog] [info] iteration = 0 | max rel diff. = 64.431
[2020-04-26 11:00:24.247] [jointLog] [info] iteration = 100 | max rel diff. = 0.00287445
[2020-04-26 11:00:24.248] [jointLog] [info] Finished optimizer
[2020-04-26 11:00:24.248] [jointLog] [info] writing output 

[2020-04-26 11:00:24.295] [jointLog] [warning] NOTE: Read Lib [[ /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-warm/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq, /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-warm/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq]] :

Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ambient_07/lib_format_counts.json for details

[2020-04-26 11:00:24.122] [fileLog] [info] 
At end of round 0
==================
Observed 30179 total fragments (30179 in most recent round)