Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
salmon
Describe the bug
is been running like an order of magnitude slower than when I last used it
A clear and concise description of what the bug is.
So I am aligning reads against Arabidopsis Thaliana, using Araport 11 annotation. I usually had 20 M reads aligned within an hour or 2. I am aligning a 46M reads library and it has been running for 20 hours using 4 threads of my humble i5-3210M and is barely on 38.5M, after 20 hours! Index was constructed with default kmer size and no decoys. I have had this problem with other libraries since upgraded from V1.0.0,

To Reproduce
I guess just try to align stuff against araport11, this particular problem comes with any fq.gz. It will take hours and hours and hours to align.

Specifically, please provide at least the following information:

• Which version of salmon was used?
  1.2.1
• How was salmon installed (compiled, downloaded executable, through bioconda)?
  downloaded executable
• Which reference (e.g. transcriptome) was used?
  Araport 11, from A. thaliana
• Which read files were used?
  regular fastq.gz ( SRR7985407)
• Which which program options were used?
  --validateMappings
  -p 4
  --seqBias
  --gcBias
  --posBias

Expected behavior
Much faster alignment, it is Salmon !!
Screenshots
this is the run info so far:

Version Info: This is the most recent version of salmon.

salmon (mapping-based) v1.2.1

[ program ] => salmon

[ command ] => quant

[ index ] => { /home/jaimealaniz/Documents/indexes/salmon/ara11/ }

[ libType ] => { A }

[ mates1 ] => { SRR7985407_1.fq.gz }

[ mates2 ] => { SRR7985407_2.fq.gz }

[ validateMappings ] => { }

[ threads ] => { 4 }

[ seqBias ] => { }

[ gcBias ] => { }

[ posBias ] => { }

[ output ] => { /home/jaimealaniz/Documents/salmon.embryo/SRR7985407/ }

Logs will be written to /home/jaimealaniz/Documents/salmon.embryo/SRR7985407/logs
[2020-05-29 20:14:24.283] [jointLog] [info] setting maxHashResizeThreads to 4
[2020-05-29 20:14:24.283] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2020-05-29 20:14:24.283] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-05-29 20:14:24.283] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-05-29 20:14:24.283] [jointLog] [info] parsing read library format
[2020-05-29 20:14:24.283] [jointLog] [info] There is 1 library.
[2020-05-29 20:14:24.341] [jointLog] [info] Loading pufferfish index
[2020-05-29 20:14:24.342] [jointLog] [info] Loading dense pufferfish index.

| Loading contig table | Time = 41.693 ms

size = 357712

| Loading contig offsets | Time = 657 us

| Loading reference lengths | Time = 202.87 us

| Loading mphf table | Time = 16.335 ms

size = 64786639
Number of ones: 357711
Number of ones per inventory item: 512
Inventory entries filled: 699

| Loading contig boundaries | Time = 154.69 ms

size = 64786639

| Loading sequence | Time = 6.3275 ms

size = 54055309

| Loading positions | Time = 68.544 ms

size = 74351806

| Loading reference sequence | Time = 7.0924 ms

| Loading reference accumulative lengths | Time = 325.83 us

[2020-05-29 20:14:24.638] [jointLog] [info] done
[2020-05-29 20:14:24.638] [jointLog] [info] Index contained 57,190 targets
[2020-05-29 20:14:25.202] [jointLog] [info] Number of decoys : 0

processed 38,500,000 fragmentsntLog] [info] Automatically detected most likely library type as IU
hits: 40,221,178, hits per frag: 1.04508

Desktop (please complete the following information):

• OS:Ubuntu
• Version 18.04

Additional context
Previously used salmon on this laptop and it was much much faster, that'ts the main reason I use salmon.