HybPhyloMaker "rapid instructions" (June 2024) 1. Log in to skirit (skirit. ics.muni.cz aka brno2) MetaCentrum frontend ssh metausername@skirit.ics.muni.cz 2. Clone HybPhyloMaker from GitHub and move HybSeqSource folder to home folder, download reference git clone https://github.com/tomas-fer/HybPhyloMaker mv HybPhyloMaker/HybSeqSource/ . cd HybSeqSource wget https://raw.githubusercontent.com/tomas-fer/HybSeqCourse/master/curcuma_HybSeqProbes_first958.fa cd ../HybPhyloMaker 3. Copy test dataset cp -r /storage/projects/botany-uk/HybSeqCourse2024 . 4. Edit file settings.cfg (Ctrl+O to save changes, Ctrl+X to exit editor) nano settings.cfg location=1 server=brno2 data=HybPhyloMaker/HybSeqCourse2024 OUTGROUP="Zingiber-officinale_S242" MISSINGPERCENT=75 SPECIESPRESENCE=40 probes=curcuma_HybSeqProbes_first958.fa raxmlperjob=1 phypartsbs=50 5. Prepare pseudoreference qsub HybPhyloMaker0b_preparereference.sh 6. Install appropriate R packages (and wait until this and previous jobs are finished) qsub HybPhyloMaker0c_Rsetup_MetaCentrum.sh 7. Filter the raw data qsub HybPhyloMaker1a_rawprocessParallel.sh 8. Run this submitter created by the previous job (this script submits 35 jobs) cd HybSeqCourse2024/20filtered/ && ./submitRawProcessJobs.sh && cd ../.. 9. Run the summary script (after all jobs are finished) qsub HybPhyloMaker1a2_rawprocessParallel_summary.sh 10. Map reads to pseudoreference qsub HybPhyloMaker2a_readmappingParallel.sh 11. Run this submitter created by the previous job (this script submits 35 jobs) cd HybSeqCourse2024/exons/21mapped_bwa/ && ./submitMappingJobs.sh && cd ../../.. 12. Run the summary script (after all jobs are finished) qsub HybPhyloMaker2a2_readmappingParallel_summary.sh 13. Generate PSLX files qsub HybPhyloMaker3_generatepslx.sh 14. Copy PSLX files mkdir pslx_HybSeqCourse2024 cp HybSeqCourse2024/exons/50pslx/*.pslx pslx_HybSeqCourse2024 15. Edit file settings.cfg nano settings.cfg otherpslx=HybPhyloMaker/pslx_HybSeqCourse2024 16. Generate exon assemblies qsub HybPhyloMaker4a_processpslx.sh 17. Filter missing data qsub HybPhyloMaker5_missingdataremoval.sh 18. Generate RAxML trees qsub HybPhyloMaker6a_RAxML_for_selected.sh 19. Run this submitter created by the previous job (this script submits 246 jobs) cd HybSeqCourse2024/exons/72trees75_40/RAxML/ && ./submitRAxMLjobs.sh && cd ../../../.. 20. Run the summary script (after all jobs are finished) qsub HybPhyloMaker6a2_RAxML_trees_summary.sh 21. Create tree files qsub HybPhyloMaker7_roottrees.sh 22. Create diverse species trees (run all four, no need to wait...) qsub HybPhyloMaker8a_astral.sh qsub HybPhyloMaker8b_astrid.sh qsub HybPhyloMaker8c_mrl.sh qsub HybPhyloMaker8e_concatenatedFastTree.sh 23. After all jobs are finished run these additional scripts qsub HybPhyloMaker8h_neighbourNetwork.sh qsub HybPhyloMaker8k_quartetsampling.sh qsub HybPhyloMaker11_phyparts.sh