[2020-04-30 07:04:44.065] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:44.065] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:44.066] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:44.066] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:44.066] [jointLog] [info] parsing read library format
[2020-04-30 07:04:44.066] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:44.133] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:44.133] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information.
[2020-04-30 07:04:44.133] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:44.247] [jointLog] [info] done
[2020-04-30 07:04:44.248] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:44.264] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:46.212] [fileLog] [info] 
At end of round 0
==================
Observed 30179 total fragments (30179 in most recent round)

[2020-04-30 07:04:46.211] [jointLog] [info] Computed 2,215 rich equivalence classes for further processing
[2020-04-30 07:04:46.211] [jointLog] [info] Counted 27,299 total reads in the equivalence classes 
[2020-04-30 07:04:46.274] [jointLog] [info] Number of mappings discarded because of alignment score : 16,363
[2020-04-30 07:04:46.274] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,386
[2020-04-30 07:04:46.274] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:46.274] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 46
[2020-04-30 07:04:46.278] [jointLog] [warning] Only 27299 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-30 07:04:46.278] [jointLog] [info] Mapping rate = 90.4569%

[2020-04-30 07:04:46.278] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:46.279] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:46.291] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:46.294] [jointLog] [info] iteration = 0 | max rel diff. = 59.9571
[2020-04-30 07:04:46.365] [jointLog] [info] iteration = 100 | max rel diff. = 0.000302898
[2020-04-30 07:04:46.365] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:46.365] [jointLog] [info] writing output 

[2020-04-30 07:04:46.443] [jointLog] [warning] NOTE: Read Lib [[ /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq, /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq]] :

Detected a *potential* strand bias > 1% in an unstranded protocol check the file: 463_quant/lib_format_counts.json for details