==** parameter inputs for pyRAD version 3.0.6 **======================== affected step == /scratch2/dm733/RADSeq/DarterRAD/deMulti_allDarters_final ## 1. Working directory (all) /fastscratch/dm733/RADSeq/RawData/Darter/PLATE_A/*.fastq.gz ## 2. Loc. of non-demultiplexed files (if not line 18) (s1) /fastscratch/dm733/RADSeq/RawData/barcodes/Near2_Darter_A_barcodes.txt ## 3. Loc. of barcode file (if not line 18) (s1) /home2/dm733/bin/vsearch ## 4. command (or path) to call vsearch (or usearch) (s3,s6) /usr/local/cluster/software/installation/muscle/muscle3.8.31_i86linux64 ## 5. command (or path) to call muscle (s3,s7) TGCAGG ## 6. Restriction overhang (e.g., C|TGCAG -> TGCAG) (s1,s2) 8 ## 7. N processors (parallel) (all) 6 ## 8. Mindepth: min coverage for a cluster (s4,s5) 4 ## 9. NQual: max # sites with qual < 20 (or see line 20)(s2) .88 ## 10. Wclust: clustering threshold as a decimal (s3,s6) rad ## 11. Datatype: rad,gbs,pairgbs,pairddrad,(others:see docs)(all) 30 ## 12. MinCov: min samples in a final locus (s7) 3 ## 13. MaxSH: max inds with shared hetero site (s7) c88d6m30p3_RAxML ## 14. Prefix name for final output (no spaces) (s7) ==== optional params below this line =================================== affected step == ## 15.opt.: select subset (prefix* only selector) (s2-s7) ## 16.opt.: add-on (outgroup) taxa (list or prefix*) (s6,s7) ## 17.opt.: exclude taxa (list or prefix*) (s7) /scratch2/dm733/RADSeq/DarterRAD/deMulti_allDarters_final/fastq ## 18.opt.: loc. of de-multiplexed data (s2) ## 19.opt.: maxM: N mismatches in barcodes (def= 1) (s1) ## 20.opt.: phred Qscore offset (def= 33) (s2) ## 21.opt.: filter: def=0=NQual 1=NQual+adapters. 2=strict (s2) ## 22.opt.: a priori E,H (def= 0.001,0.01, if not estimated) (s5) ## 23.opt.: maxN: max Ns in a cons seq (def=5) (s5) ## 24.opt.: maxH: max heterozyg. sites in cons seq (def=5) (s5) ## 25.opt.: ploidy: max alleles in cons seq (def=2;see docs) (s4,s5) ## 26.opt.: maxSNPs: (def=100). Paired (def=100,100) (s7) ## 27.opt.: maxIndels: within-clust,across-clust (def. 3,99) (s3,s7) ## 28.opt.: random number seed (def. 112233) (s3,s6,s7) ## 29.opt.: trim overhang left,right on final loci, def(0,0) (s7) n,p,k ## 30.opt.: output formats: p,n,a,s,v,u,t,m,k,g,* (see docs) (s7) ## 31.opt.: maj. base call at depth>x