PhyloAcc pre-run stats
1. Run info (st-test-branches)

The PhyloAcc interface was run on Sunday Oct 23, 2022 at 10:03:51 EDT on as follows:

/n/home07/gthomas/anaconda3/envs/phyloacc-pkg/bin/ -d /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/mammal-input-accelerated/seq/ -m /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/mammal-input-accelerated/mammal_acc1.mod -t turTru2;orcOrc1;odoRosDiv1;lepWed1;triMan1 -g monDom5;sarHar1;macEug2;ornAna1 -r st -burnin 1000 -mcmc 7000 -n 24 -p 8 -j 20 -batch 25 -part holy-info,shared,holy-smokes -time 24 -o /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/st-test-branches/ -phyloacc CONSERVE_PRIOR_B 0.1;ACCE_PRIOR_A 4; ACCE_PRIOR_B 0.5; CONSERVE_PROP 0.5; CONSERVE_RATE 0.3; TRIM_GAP_PERCENT 0.7 --overwrite
Alignment and batch info
Input alignments 2030
Alignments with 0 informative sites (removed) 1
Alignments for species tree model 2029
Alignments for gene tree model 0
Batches 82
Alignments per batch 25
Processes to use per batch 8
Batches using species tree model 82
Batches using gene tree model 0
Batches to submit to cluster simultaneously 20

See the full log file for more info.

Below are some summary plots. Raw data is also available in CSV format in the alignment stats file.

Run batches

The generated batches can be run with Snakemake with the following command:

snakemake -p -s /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/st-test-branches/phyloacc-job-files/snakemake/run_phyloacc.smk --configfile /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/st-test-branches/phyloacc-job-files/snakemake/phyloacc-config.yaml --profile /n/holylfs05/LABS/informatics/Everyone/phyloacc-data/workshop-20221027/mammal/st-test-branches/phyloacc-job-files/snakemake/profiles/slurm_profile --dryrun

Note that this includes the --dryrun option to check for possible errors before submitting jobs. If everything looks good after running that, feel free to remove the --dryrun option to submit the jobs to your cluster. You may also want to run this in the background using screen, tmux or some other terminal multiplexer to avoid disruptions due to server disconnects.

2. Input species tree
Species 62
Target species 5
Conserved species 53
Outgroup species 4
3. Distribution of locus lengths
Average alignment length 129.627
Median alignment length 92.0
Average sequence length (no gaps) per alignment 128.71
Median sequence length (no gaps) per alignment 90.742
4. Distribution of informative sites per locus
5. Correlation between variable and informative sites