<div dir="ltr"><div dir="ltr"><div><div>Dear MAKER Team,</div><div><br></div><div>I am running MAKER 2.31.10 a 32 core instance. I followed the Post Processing of Annotations steps as described in the MAKER Tutorial for GMOD Online Training 2014 as best I could, but I get an error when I run maker_functional_gff. The commands in the order of execution and relevant output are shown below.</div><div><br></div><div>Where did I do wrong? </div><div><br></div><div># run blastp command</div><div>blastp -query genome.all.maker.proteins.fasta -db uniprot_sprot.fasta -num_threads 32 -evalue 1e-6 -max_hsps 1 -max_target_seqs 1 -outfmt 6 -out output.blastp</div><div><br></div><div># run interproscan command</div><div>interproscan.sh -appl pfam -dp -f TSV -goterms -iprlookup -pa -t p -i genome.all.maker.proteins.fasta -o output.iprscan</div><div><br></div><div># create naming table</div><div>maker_map_ids --prefix ThuMac --justify 5  genome.all.gff > genome.all.map</div><div><br></div><div># copy files for safe keeping</div><div>cp genome.all.gff genome.all.renamed.gff</div><div>cp genome.all.noseq.gff genome.all.noseq.renamed.gff</div><div>cp genome.all.maker.proteins.fasta genome.all.maker.proteins.renamed.fasta</div><div>cp genome.all.maker.proteins.aed.0.50.fasta genome.all.maker.proteins.aed.0.50.renamed.fasta</div><div>cp genome.all.maker.unique.proteins.aed.0.50.fasta genome.all.maker.unique.proteins.aed.0.50.renamed.fasta</div><div>cp genome.all.maker.transcripts.fasta genome.all.maker.transcripts.renamed.fasta</div><div>cp genome.all.maker.transcripts.aed.0.50.fasta genome.all.maker.transcripts.aed.0.50.renamed.fasta</div><div>cp output.iprscan output.renamed.iprscan </div><div>cp output.blastp output.renamed.blastp</div><div><br></div><div># replace uninformative MAKER protein/transcript names with useful ones</div><div>map_gff_ids genome.all.map genome.all.renamed.gff</div><div>map_gff_ids genome.all.map genome.all.noseq.renamed.gff</div><div>map_fasta_ids genome.all.map genome.all.maker.proteins.renamed.fasta</div><div>map_fasta_ids genome.all.map genome.all.maker.proteins.aed.0.50.renamed.fasta</div><div>map_fasta_ids genome.all.map genome.all.maker.unique.proteins.aed.0.50.renamed.fasta</div><div>map_fasta_ids genome.all.map genome.all.maker.transcripts.renamed.fasta</div><div>map_fasta_ids genome.all.map genome.all.maker.transcripts.aed.0.50.renamed.fasta</div><div>map_data_ids genome.all.map output.renamed.iprscan</div><div>map_data_ids genome.all.map output.renamed.blastp</div><div><br></div><div># assign annotations</div><div>maker_functional_gff uniprot_sprot.db output.renamed.blastp genome.all.renamed.gff > genome.all.renamed.putative_function.gff</div><div><br></div><div>> head output.renamed.blastp</div><div>ThuMac30929-RA<span style="white-space:pre">  </span>P20036<span style="white-space:pre">       </span>41.791<span style="white-space:pre">       </span>134<span style="white-space:pre">  </span>77<span style="white-space:pre">   </span>1<span style="white-space:pre">    </span>326<span style="white-space:pre">  </span>458<span style="white-space:pre">  </span>113<span style="white-space:pre">  </span>246<span style="white-space:pre">  </span>9.51e-28<span style="white-space:pre">     </span>114</div><div>ThuMac19623-RA<span style="white-space:pre">     </span>P81018<span style="white-space:pre">       </span>35.714<span style="white-space:pre">       </span>168<span style="white-space:pre">  </span>87<span style="white-space:pre">   </span>2<span style="white-space:pre">    </span>1<span style="white-space:pre">    </span>147<span style="white-space:pre">  </span>1<span style="white-space:pre">    </span>168<span style="white-space:pre">  </span>8.40e-33<span style="white-space:pre">     </span>117</div><div>ThuMac19629-RA<span style="white-space:pre">     </span>Q66I51<span style="white-space:pre">       </span>68.939<span style="white-space:pre">       </span>264<span style="white-space:pre">  </span>79<span style="white-space:pre">   </span>2<span style="white-space:pre">    </span>1<span style="white-space:pre">    </span>263<span style="white-space:pre">  </span>1<span style="white-space:pre">    </span>262<span style="white-space:pre">  </span>1.48e-130<span style="white-space:pre">    </span>372</div><div>ThuMac19628-RA<span style="white-space:pre">     </span>Q61464<span style="white-space:pre">       </span>55.172<span style="white-space:pre">       </span>87<span style="white-space:pre">   </span>37<span style="white-space:pre">   </span>1<span style="white-space:pre">    </span>766<span style="white-space:pre">  </span>852<span style="white-space:pre">  </span>382<span style="white-space:pre">  </span>466<span style="white-space:pre">  </span>4.42e-25<span style="white-space:pre">     </span>119</div><div>ThuMac19627-RA<span style="white-space:pre">     </span>P07898<span style="white-space:pre">       </span>48.276<span style="white-space:pre">       </span>58<span style="white-space:pre">   </span>29<span style="white-space:pre">   </span>1<span style="white-space:pre">    </span>13<span style="white-space:pre">   </span>69<span style="white-space:pre">   </span>1962<span style="white-space:pre"> </span>2019<span style="white-space:pre"> </span>3.60e-13<span style="white-space:pre">     </span>65.9</div><div>ThuMac19626-RA<span style="white-space:pre">    </span>P81018<span style="white-space:pre">       </span>36.782<span style="white-space:pre">       </span>174<span style="white-space:pre">  </span>96<span style="white-space:pre">   </span>2<span style="white-space:pre">    </span>21<span style="white-space:pre">   </span>180<span style="white-space:pre">  </span>1<span style="white-space:pre">    </span>174<span style="white-space:pre">  </span>5.75e-36<span style="white-space:pre">     </span>127</div><div>ThuMac19624-RA<span style="white-space:pre">     </span>P81018<span style="white-space:pre">       </span>35.057<span style="white-space:pre">       </span>174<span style="white-space:pre">  </span>99<span style="white-space:pre">   </span>2<span style="white-space:pre">    </span>21<span style="white-space:pre">   </span>180<span style="white-space:pre">  </span>1<span style="white-space:pre">    </span>174<span style="white-space:pre">  </span>2.19e-33<span style="white-space:pre">     </span>120</div><div>ThuMac19625-RA<span style="white-space:pre">     </span>Q28343<span style="white-space:pre">       </span>32.520<span style="white-space:pre">       </span>123<span style="white-space:pre">  </span>43<span style="white-space:pre">   </span>2<span style="white-space:pre">    </span>35<span style="white-space:pre">   </span>117<span style="white-space:pre">  </span>2123<span style="white-space:pre"> </span>2245<span style="white-space:pre"> </span>7.57e-17<span style="white-space:pre">     </span>78.6</div><div>ThuMac19636-RA<span style="white-space:pre">    </span>Q9QX29<span style="white-space:pre">       </span>90.909<span style="white-space:pre">       </span>110<span style="white-space:pre">  </span>10<span style="white-space:pre">   </span>0<span style="white-space:pre">    </span>5<span style="white-space:pre">    </span>114<span style="white-space:pre">  </span>458<span style="white-space:pre">  </span>567<span style="white-space:pre">  </span>6.45e-65<span style="white-space:pre">     </span>216</div><div>ThuMac19638-RA<span style="white-space:pre">     </span>Q9QX29<span style="white-space:pre">       </span>57.391<span style="white-space:pre">       </span>115<span style="white-space:pre">  </span>35<span style="white-space:pre">   </span>3<span style="white-space:pre">    </span>5<span style="white-space:pre">    </span>114<span style="white-space:pre">  </span>703<span style="white-space:pre">  </span>808<span style="white-space:pre">  </span>3.06e-28<span style="white-space:pre">     </span>120</div><div><br></div><div>> head output.renamed.iprscan </div><div>ThuMac08407-RA<span style="white-space:pre">   </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre">     </span>631<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF00520<span style="white-space:pre">      </span>Ion transport protein<span style="white-space:pre">        </span>154<span style="white-space:pre">  </span>413<span style="white-space:pre">  </span>3.8E-21<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR005821<span style="white-space:pre">    </span>Ion transport domain<span style="white-space:pre"> </span>GO:0005216|GO:0006811|GO:0016020|GO:0055085</div><div>ThuMac08407-RA<span style="white-space:pre">     </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre">     </span>631<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF08412<span style="white-space:pre">      </span>Ion transport protein N-terminal<span style="white-space:pre">     </span>109<span style="white-space:pre">  </span>152<span style="white-space:pre">  </span>5.1E-19<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR013621<span style="white-space:pre">    </span>Ion transport N-terminal<span style="white-space:pre">             </span>Reactome: R-HSA-1296061</div><div>ThuMac08407-RA<span style="white-space:pre"> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre">     </span>631<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF00027<span style="white-space:pre">      </span>Cyclic nucleotide-binding domain<span style="white-space:pre">     </span>519<span style="white-space:pre">  </span>601<span style="white-space:pre">  </span>1.0E-17<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR000595<span style="white-space:pre">    </span>Cyclic nucleotide-binding domain</div><div>ThuMac24094-RA<span style="white-space:pre">        </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre">     </span>414<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF13765<span style="white-space:pre">      </span>SPRY-associated domain<span style="white-space:pre">       </span>235<span style="white-space:pre">  </span>283<span style="white-space:pre">  </span>8.9E-23<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR006574<span style="white-space:pre">    </span>SPRY-associated</div><div>ThuMac24094-RA<span style="white-space:pre"> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre">     </span>414<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF00643<span style="white-space:pre">      </span>B-box zinc finger<span style="white-space:pre">    </span>18<span style="white-space:pre">   </span>56<span style="white-space:pre">   </span>5.2E-12<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR000315<span style="white-space:pre">    </span>B-box-type zinc finger<span style="white-space:pre">       </span>GO:0008270</div><div>ThuMac24094-RA<span style="white-space:pre">      </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre">     </span>414<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF00622<span style="white-space:pre">      </span>SPRY domain<span style="white-space:pre">  </span>287<span style="white-space:pre">  </span>391<span style="white-space:pre">  </span>2.2E-14<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR003877<span style="white-space:pre">    </span>SPRY domain<span style="white-space:pre">  </span>GO:0005515</div><div>ThuMac08369-RA<span style="white-space:pre">      </span>7aee1da5a47975ab8e43b68bfd1a117c<span style="white-space:pre">     </span>139<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF00076<span style="white-space:pre">      </span>RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)<span style="white-space:pre">      </span>22<span style="white-space:pre">   </span>87<span style="white-space:pre">   </span>1.6E-15<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR000504<span style="white-space:pre">    </span>RNA recognition motif domain<span style="white-space:pre"> </span>GO:0003676</div><div>ThuMac26054-RA<span style="white-space:pre">      </span>8f4119609312bd6442f8bb094c104231<span style="white-space:pre">     </span>462<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF07565<span style="white-space:pre">      </span>Band 3 cytoplasmic domain<span style="white-space:pre">    </span>173<span style="white-space:pre">  </span>443<span style="white-space:pre">  </span>7.3E-100<span style="white-space:pre">     </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR013769<span style="white-space:pre">    </span>Band 3 cytoplasmic domain<span style="white-space:pre">    </span>GO:0006820|GO:0008509|GO:0016021<span style="white-space:pre">     </span>Reactome: R-HSA-425381</div><div>ThuMac07958-RA<span style="white-space:pre">  </span>d2b749fa573a5e452cadee56090c9588<span style="white-space:pre">     </span>804<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF03372<span style="white-space:pre">      </span>Endonuclease/Exonuclease/phosphatase family<span style="white-space:pre">  </span>235<span style="white-space:pre">  </span>535<span style="white-space:pre">  </span>7.0E-11<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR005135<span style="white-space:pre">    </span>Endonuclease/exonuclease/phosphatase</div><div>ThuMac07958-RA<span style="white-space:pre">    </span>d2b749fa573a5e452cadee56090c9588<span style="white-space:pre">     </span>804<span style="white-space:pre">  </span>Pfam<span style="white-space:pre"> </span>PF17751<span style="white-space:pre">      </span>SKICH domain<span style="white-space:pre"> </span>555<span style="white-space:pre">  </span>649<span style="white-space:pre">  </span>9.8E-23<span style="white-space:pre">      </span>T<span style="white-space:pre">    </span>18-04-2019<span style="white-space:pre">   </span>IPR041611<span style="white-space:pre">    </span>SKICH domain</div><div><br></div><div>> map_data_ids genome.all.map output.renamed.iprscan</div><div>WARNING: No mapping available for ThuMac01937-RA</div><div>WARNING: No mapping available for ThuMac02226-RA</div><div>WARNING: No mapping available for ThuMac20730-RA</div><div>WARNING: No mapping available for ThuMac20730-RA</div><div>WARNING: No mapping available for ThuMac14750-RA</div><div>(Thousands of warnings like these were returned)</div><div><br></div><div>> maker_functional_gff uniprot_sprot.db output.renamed.blastp genome.all.renamed.gff > genome.all.renamed.putative_function.gff</div><div>Can't use string ("") as a HASH ref while "strict refs" in use at /root/maker/bin/maker_functional_gff line 55, <$IN> line 3.</div><div><br></div><div>> head genome.all.renamed.putative_function.gff</div><div>##gff-version 3</div><div>scf7180000008677_pilon_pilon<span style="white-space:pre">      </span>.<span style="white-space:pre">    </span>contig<span style="white-space:pre">       </span>1<span style="white-space:pre">    </span>49996<span style="white-space:pre">        </span>.<span style="white-space:pre">    </span>.<span style="white-space:pre">    </span>.<span style="white-space:pre">    </span>ID=scf7180000008677_pilon_pilon;Name=scf7180000008677_pilon_pilon</div></div><div><br></div><div>Thanks in Advance,</div><div><br></div><div>Paul Sheridan</div><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr">CSO at Tupac Bio<div>Email: paul@tupac.bio</div><div>Homepage: <a href="http://www.paulsheridan.net" target="_blank">www.paulsheridan.net</a></div><div>Mobile: +81 80 7889 0859</div></div></div></div></div>