<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don’t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example.<br class=""><div class=""><br class=""></div><div class="">Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm.</div><div class=""><br class=""></div><div class="">Also check your input GFF3 for duplicates, as those will iteratively feed into the next run.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""> </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 18, 2016, at 9:20 AM, Matt Simenc <<a href="mailto:mcsimenc@gmail.com" class="">mcsimenc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span style="font-size:12.8000001907349px" class="">Update:</span><div style="font-size:12.8000001907349px" class=""><br class=""></div><div style="font-size:12.8000001907349px" class="">So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. </div><div style="font-size:12.8000001907349px" class=""><br class=""></div><div style="font-size:12.8000001907349px" class="">However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features.</div><div style="font-size:12.8000001907349px" class=""><br class=""></div><div style="font-size:12.8000001907349px" class="">Thanks!</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc <span dir="ltr" class=""><<a href="mailto:mcsimenc@gmail.com" target="_blank" class="">mcsimenc@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates.<span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">Matt</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc <span dir="ltr" class=""><<a href="mailto:mcsimenc@gmail.com" target="_blank" class="">mcsimenc@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this:<div class=""><br class=""></div><div class=""><p class="">maker_gff=previous_run.gff</p><p class="">est_pass=1</p><p class="">altest_pass=1</p><p class="">protein_pass=1</p><p class="">rm_pass=1</p><p class="">model_pass=1</p><p class="">pred_pass=1</p><p class="">other_pass=0</p><p class=""><br class=""></p><p class="">Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong?</p><p class=""><br class=""></p><p class="">Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models:</p><p class="">-------------------------------------<br class=""></p><p class=""><b class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>136647<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704</b></p><p class=""><b class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>136647<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704</b></p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>138512<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>138297<span class=""> </span>138361<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>137723<span class=""> </span>137786<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>137578<span class=""> </span>137643<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>136647<span class=""> </span>136871<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>138512<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>138297<span class=""> </span>138361<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>137723<span class=""> </span>137786<span class=""> </span>.<span class=""> </span>-<span class=""> </span>1<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>137578<span class=""> </span>137643<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>136647<span class=""> </span>136871<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1</p><p class=""><b class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>98236<span class=""> </span>98541<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18</b></p><div class="">
<br class="webkit-block-placeholder"></div><p class=""><b class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>98236<span class=""> </span>98541<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18</b></p><p class=""><br class=""></p><p class=""><br class=""></p><p class=""><br class=""></p><p class=""><b class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>4775142<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976</b></p><p class=""><b class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>4775142<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976</b></p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>4775142<span class=""> </span>4775330<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>4775354<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>4775142<span class=""> </span>4775330<span class=""> </span>.<span class=""> </span>+<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>4775354<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1</p><p class=""><b class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624</b></p><p class=""><b class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624</b></p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">Sacu_v1_s0004<span class=""> </span>snap_masked<span class=""> </span>match<span class=""> </span>4775142<span class=""> </span>4775554<span class=""> </span>14.976<span class=""> </span>+<span class=""> </span>.<span class=""> </span>ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976</p><p class=""><br class=""></p><p class="">Here the models' headers from the maker.proteins.fasta:</p><p class="">-------------------------------------<br class=""></p><p class="">>snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">>snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60</p><p class="">>snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">>snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101</p><p class=""><br class=""></p><p class=""><br class=""></p><p class="">Thanks!</p><span class=""><font color="#888888" class=""><p class="">Matt</p>
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