<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Sorry for the slow reply. Please capture and send the STDERR from one of the failures.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 11, 2020, at 9:12 AM, Megan Breitbach <<a href="mailto:mbreitbach@hudsonalpha.org" class="">mbreitbach@hudsonalpha.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Good morning, <div class=""><br class=""></div><div class="">I'm trying to de novo annotate a genome with ~100,000 scaffolds and a scaffold N50 of 189,900 using Maker. I've been able to use MPICH to parallelize the first round of <aker, and it will finish in ~2 weeks. However, I'm trying to improve the annotation using SNAP and when I do so every scaffold fails. I'm wondering if you could give me any advice or tell me what I might be doing wrong? </div><div class=""><br class=""></div><div class="">Here are the parameters used in the maker_opts.ctl file- </div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----Genome (these are always required)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">genome=blackbear_DNAzoo.FINAL.fasta #genome sequence (fasta file or fasta embeded in GFF3 file)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----Re-annotation Using MAKER Derived GFF3</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">maker_gff=</span><span style="font-variant-ligatures:no-common-ligatures" class="">blackbear_DNAzoo.FINAL.all.gff </span><span style="font-variant-ligatures:no-common-ligatures" class="">#MAKER derived GFF3 file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">rm_pass=1 #use repeats in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----EST Evidence (for best results provide a file for at least one)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">est=Ursus_maritimus.UrsMar_1.0.cdna.all.fa #set of ESTs or assembled mRNA-seq in fasta format</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">altest= #EST/cDNA sequence file in fasta format from an alternate organism</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----Protein Homology Evidence (for best results provide a file for at least one)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">protein=Ursus_maritimus.UrsMar_1.0.pep.all.fa<span class="gmail-Apple-converted-space"> </span>#protein sequence file in fasta format (i.e. from mutiple organisms)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">protein_gff=<span class="gmail-Apple-converted-space"> </span>#aligned protein homology evidence from an external GFF3 file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----Repeat Masking (leave values blank to skip repeat masking)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">model_org=all #select a model organism for RepBase masking in RepeatMasker</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">rm_gff= #pre-identified repeat elements from an external GFF3 file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----Gene Prediction</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">snaphmm=</span><span style="font-variant-ligatures:no-common-ligatures" class="">blackbear.hmm</span><span style="font-variant-ligatures:no-common-ligatures" class=""> #SNAP HMM file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">gmhmm= #GeneMark HMM file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">augustus_species= #Augustus gene prediction species model</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">fgenesh_par_file= #FGENESH parameter file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">pred_gff= #ab-initio predictions from an external GFF3 file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">run_evm=0 #run EvidenceModeler, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">snoscan_meth= #-O-methylation site fileto have Snoscan find snoRNAs</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">allow_overlap=0 #allowed gene overlap fraction (value from 0 to 1, blank for default)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----Other Annotation Feature Types (features MAKER doesn't recognize)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">other_gff= #extra features to pass-through to final MAKER generated GFF3 file</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----External Application Behavior Options</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#-----MAKER Behavior Options</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">min_contig=1 #skip genome contigs below this length (under 10kb are often useless)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">pred_flank=200 #flank for extending evidence clusters sent to gene predictors</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">pred_stats=1 #report AED and QI statistics for all predictions as well as models</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">min_protein=0 #require at least this many amino acids in predicted proteins</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">keep_preds=1 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">min_intron=20 #minimum intron length (used for alignment polishing)</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">tries=2 #number of times to try a contig if there is a failure for some reason</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">TMP= #specify a directory other than the system default temporary directory for temporary files</span></div><div class=""><br class=""></div><div class="">Thanks,</div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Megan Ramaker, PhD<div class="">Postdoctoral Trainee<br class=""><div class="">HudsonAlpha Institute for Biotechnology</div><div class="">601 Genome Way</div><div class="">Huntsville, AL 35806</div></div><div class="">478-284-6723</div></div></div></div></div></div></div>
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