<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="">This “WARNING: No mapping available for ThuMac01937-RA” means you are running on a file that already has been renamed. The file will have names like maker-SDFGDG-gene-0.1-mRNA-1 for example, and it’s finding the name ThuMac01937-RA, which is not in the first column of the map file. So it throws a warning.<div class=""><br class=""></div><div class="">The second one —> 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 class=""><br class=""></div><div class=""><br class=""></div><div class="">You likely have a trucated line in the GFF3. It’s missing an ID= tag. This can sometimes happen if writing to network mounted (NFS) file systems because of an ansyncrounous IO error. NFS file systems have a performance enhancement where they return SUCCESS on IO operations even and then complete the IO operation later in the background. This improves speed by letting the program advance by not blocking for the IO operation, but it reduces reliability because if the later operation is not really successful, it can’t go back and tell the program “never mind it failed.” The result is a silent truncation of data. Not super common, but not all that rare either depending on IO load (i.e. heavy MPI with lots of writes). Find the line that’s truncated, then rerun just that contig before building the merged gff3 for everything.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""> </div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 18, 2019, at 3:23 AM, Paul Sheridan <<a href="mailto:paul@tupac.bio" class="">paul@tupac.bio</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class="">Dear MAKER Team,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Where did I do wrong? </div><div class=""><br class=""></div><div class=""># run blastp command</div><div class="">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 class=""><br class=""></div><div class=""># run interproscan command</div><div class="">interproscan.sh -appl pfam -dp -f TSV -goterms -iprlookup -pa -t p -i genome.all.maker.proteins.fasta -o output.iprscan</div><div class=""><br class=""></div><div class=""># create naming table</div><div class="">maker_map_ids --prefix ThuMac --justify 5 genome.all.gff > genome.all.map</div><div class=""><br class=""></div><div class=""># copy files for safe keeping</div><div class="">cp genome.all.gff genome.all.renamed.gff</div><div class="">cp genome.all.noseq.gff genome.all.noseq.renamed.gff</div><div class="">cp genome.all.maker.proteins.fasta genome.all.maker.proteins.renamed.fasta</div><div class="">cp genome.all.maker.proteins.aed.0.50.fasta genome.all.maker.proteins.aed.0.50.renamed.fasta</div><div class="">cp genome.all.maker.unique.proteins.aed.0.50.fasta genome.all.maker.unique.proteins.aed.0.50.renamed.fasta</div><div class="">cp genome.all.maker.transcripts.fasta genome.all.maker.transcripts.renamed.fasta</div><div class="">cp genome.all.maker.transcripts.aed.0.50.fasta genome.all.maker.transcripts.aed.0.50.renamed.fasta</div><div class="">cp output.iprscan output.renamed.iprscan </div><div class="">cp output.blastp output.renamed.blastp</div><div class=""><br class=""></div><div class=""># replace uninformative MAKER protein/transcript names with useful ones</div><div class="">map_gff_ids genome.all.map genome.all.renamed.gff</div><div class="">map_gff_ids genome.all.map genome.all.noseq.renamed.gff</div><div class="">map_fasta_ids genome.all.map genome.all.maker.proteins.renamed.fasta</div><div class="">map_fasta_ids genome.all.map genome.all.maker.proteins.aed.0.50.renamed.fasta</div><div class="">map_fasta_ids genome.all.map genome.all.maker.unique.proteins.aed.0.50.renamed.fasta</div><div class="">map_fasta_ids genome.all.map genome.all.maker.transcripts.renamed.fasta</div><div class="">map_fasta_ids genome.all.map genome.all.maker.transcripts.aed.0.50.renamed.fasta</div><div class="">map_data_ids genome.all.map output.renamed.iprscan</div><div class="">map_data_ids genome.all.map output.renamed.blastp</div><div class=""><br class=""></div><div class=""># assign annotations</div><div class="">maker_functional_gff uniprot_sprot.db output.renamed.blastp genome.all.renamed.gff > genome.all.renamed.putative_function.gff</div><div class=""><br class=""></div><div class="">> head output.renamed.blastp</div><div class="">ThuMac30929-RA<span style="white-space:pre" class=""> </span>P20036<span style="white-space:pre" class=""> </span>41.791<span style="white-space:pre" class=""> </span>134<span style="white-space:pre" class=""> </span>77<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>326<span style="white-space:pre" class=""> </span>458<span style="white-space:pre" class=""> </span>113<span style="white-space:pre" class=""> </span>246<span style="white-space:pre" class=""> </span>9.51e-28<span style="white-space:pre" class=""> </span>114</div><div class="">ThuMac19623-RA<span style="white-space:pre" class=""> </span>P81018<span style="white-space:pre" class=""> </span>35.714<span style="white-space:pre" class=""> </span>168<span style="white-space:pre" class=""> </span>87<span style="white-space:pre" class=""> </span>2<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>147<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>168<span style="white-space:pre" class=""> </span>8.40e-33<span style="white-space:pre" class=""> </span>117</div><div class="">ThuMac19629-RA<span style="white-space:pre" class=""> </span>Q66I51<span style="white-space:pre" class=""> </span>68.939<span style="white-space:pre" class=""> </span>264<span style="white-space:pre" class=""> </span>79<span style="white-space:pre" class=""> </span>2<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>263<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>262<span style="white-space:pre" class=""> </span>1.48e-130<span style="white-space:pre" class=""> </span>372</div><div class="">ThuMac19628-RA<span style="white-space:pre" class=""> </span>Q61464<span style="white-space:pre" class=""> </span>55.172<span style="white-space:pre" class=""> </span>87<span style="white-space:pre" class=""> </span>37<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>766<span style="white-space:pre" class=""> </span>852<span style="white-space:pre" class=""> </span>382<span style="white-space:pre" class=""> </span>466<span style="white-space:pre" class=""> </span>4.42e-25<span style="white-space:pre" class=""> </span>119</div><div class="">ThuMac19627-RA<span style="white-space:pre" class=""> </span>P07898<span style="white-space:pre" class=""> </span>48.276<span style="white-space:pre" class=""> </span>58<span style="white-space:pre" class=""> </span>29<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>13<span style="white-space:pre" class=""> </span>69<span style="white-space:pre" class=""> </span>1962<span style="white-space:pre" class=""> </span>2019<span style="white-space:pre" class=""> </span>3.60e-13<span style="white-space:pre" class=""> </span>65.9</div><div class="">ThuMac19626-RA<span style="white-space:pre" class=""> </span>P81018<span style="white-space:pre" class=""> </span>36.782<span style="white-space:pre" class=""> </span>174<span style="white-space:pre" class=""> </span>96<span style="white-space:pre" class=""> </span>2<span style="white-space:pre" class=""> </span>21<span style="white-space:pre" class=""> </span>180<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>174<span style="white-space:pre" class=""> </span>5.75e-36<span style="white-space:pre" class=""> </span>127</div><div class="">ThuMac19624-RA<span style="white-space:pre" class=""> </span>P81018<span style="white-space:pre" class=""> </span>35.057<span style="white-space:pre" class=""> </span>174<span style="white-space:pre" class=""> </span>99<span style="white-space:pre" class=""> </span>2<span style="white-space:pre" class=""> </span>21<span style="white-space:pre" class=""> </span>180<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>174<span style="white-space:pre" class=""> </span>2.19e-33<span style="white-space:pre" class=""> </span>120</div><div class="">ThuMac19625-RA<span style="white-space:pre" class=""> </span>Q28343<span style="white-space:pre" class=""> </span>32.520<span style="white-space:pre" class=""> </span>123<span style="white-space:pre" class=""> </span>43<span style="white-space:pre" class=""> </span>2<span style="white-space:pre" class=""> </span>35<span style="white-space:pre" class=""> </span>117<span style="white-space:pre" class=""> </span>2123<span style="white-space:pre" class=""> </span>2245<span style="white-space:pre" class=""> </span>7.57e-17<span style="white-space:pre" class=""> </span>78.6</div><div class="">ThuMac19636-RA<span style="white-space:pre" class=""> </span>Q9QX29<span style="white-space:pre" class=""> </span>90.909<span style="white-space:pre" class=""> </span>110<span style="white-space:pre" class=""> </span>10<span style="white-space:pre" class=""> </span>0<span style="white-space:pre" class=""> </span>5<span style="white-space:pre" class=""> </span>114<span style="white-space:pre" class=""> </span>458<span style="white-space:pre" class=""> </span>567<span style="white-space:pre" class=""> </span>6.45e-65<span style="white-space:pre" class=""> </span>216</div><div class="">ThuMac19638-RA<span style="white-space:pre" class=""> </span>Q9QX29<span style="white-space:pre" class=""> </span>57.391<span style="white-space:pre" class=""> </span>115<span style="white-space:pre" class=""> </span>35<span style="white-space:pre" class=""> </span>3<span style="white-space:pre" class=""> </span>5<span style="white-space:pre" class=""> </span>114<span style="white-space:pre" class=""> </span>703<span style="white-space:pre" class=""> </span>808<span style="white-space:pre" class=""> </span>3.06e-28<span style="white-space:pre" class=""> </span>120</div><div class=""><br class=""></div><div class="">> head output.renamed.iprscan </div><div class="">ThuMac08407-RA<span style="white-space:pre" class=""> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre" class=""> </span>631<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF00520<span style="white-space:pre" class=""> </span>Ion transport protein<span style="white-space:pre" class=""> </span>154<span style="white-space:pre" class=""> </span>413<span style="white-space:pre" class=""> </span>3.8E-21<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR005821<span style="white-space:pre" class=""> </span>Ion transport domain<span style="white-space:pre" class=""> </span>GO:0005216|GO:0006811|GO:0016020|GO:0055085</div><div class="">ThuMac08407-RA<span style="white-space:pre" class=""> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre" class=""> </span>631<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF08412<span style="white-space:pre" class=""> </span>Ion transport protein N-terminal<span style="white-space:pre" class=""> </span>109<span style="white-space:pre" class=""> </span>152<span style="white-space:pre" class=""> </span>5.1E-19<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR013621<span style="white-space:pre" class=""> </span>Ion transport N-terminal<span style="white-space:pre" class=""> </span>Reactome: R-HSA-1296061</div><div class="">ThuMac08407-RA<span style="white-space:pre" class=""> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre" class=""> </span>631<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF00027<span style="white-space:pre" class=""> </span>Cyclic nucleotide-binding domain<span style="white-space:pre" class=""> </span>519<span style="white-space:pre" class=""> </span>601<span style="white-space:pre" class=""> </span>1.0E-17<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR000595<span style="white-space:pre" class=""> </span>Cyclic nucleotide-binding domain</div><div class="">ThuMac24094-RA<span style="white-space:pre" class=""> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre" class=""> </span>414<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF13765<span style="white-space:pre" class=""> </span>SPRY-associated domain<span style="white-space:pre" class=""> </span>235<span style="white-space:pre" class=""> </span>283<span style="white-space:pre" class=""> </span>8.9E-23<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR006574<span style="white-space:pre" class=""> </span>SPRY-associated</div><div class="">ThuMac24094-RA<span style="white-space:pre" class=""> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre" class=""> </span>414<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF00643<span style="white-space:pre" class=""> </span>B-box zinc finger<span style="white-space:pre" class=""> </span>18<span style="white-space:pre" class=""> </span>56<span style="white-space:pre" class=""> </span>5.2E-12<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR000315<span style="white-space:pre" class=""> </span>B-box-type zinc finger<span style="white-space:pre" class=""> </span>GO:0008270</div><div class="">ThuMac24094-RA<span style="white-space:pre" class=""> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre" class=""> </span>414<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF00622<span style="white-space:pre" class=""> </span>SPRY domain<span style="white-space:pre" class=""> </span>287<span style="white-space:pre" class=""> </span>391<span style="white-space:pre" class=""> </span>2.2E-14<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR003877<span style="white-space:pre" class=""> </span>SPRY domain<span style="white-space:pre" class=""> </span>GO:0005515</div><div class="">ThuMac08369-RA<span style="white-space:pre" class=""> </span>7aee1da5a47975ab8e43b68bfd1a117c<span style="white-space:pre" class=""> </span>139<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF00076<span style="white-space:pre" class=""> </span>RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)<span style="white-space:pre" class=""> </span>22<span style="white-space:pre" class=""> </span>87<span style="white-space:pre" class=""> </span>1.6E-15<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR000504<span style="white-space:pre" class=""> </span>RNA recognition motif domain<span style="white-space:pre" class=""> </span>GO:0003676</div><div class="">ThuMac26054-RA<span style="white-space:pre" class=""> </span>8f4119609312bd6442f8bb094c104231<span style="white-space:pre" class=""> </span>462<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF07565<span style="white-space:pre" class=""> </span>Band 3 cytoplasmic domain<span style="white-space:pre" class=""> </span>173<span style="white-space:pre" class=""> </span>443<span style="white-space:pre" class=""> </span>7.3E-100<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR013769<span style="white-space:pre" class=""> </span>Band 3 cytoplasmic domain<span style="white-space:pre" class=""> </span>GO:0006820|GO:0008509|GO:0016021<span style="white-space:pre" class=""> </span>Reactome: R-HSA-425381</div><div class="">ThuMac07958-RA<span style="white-space:pre" class=""> </span>d2b749fa573a5e452cadee56090c9588<span style="white-space:pre" class=""> </span>804<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF03372<span style="white-space:pre" class=""> </span>Endonuclease/Exonuclease/phosphatase family<span style="white-space:pre" class=""> </span>235<span style="white-space:pre" class=""> </span>535<span style="white-space:pre" class=""> </span>7.0E-11<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR005135<span style="white-space:pre" class=""> </span>Endonuclease/exonuclease/phosphatase</div><div class="">ThuMac07958-RA<span style="white-space:pre" class=""> </span>d2b749fa573a5e452cadee56090c9588<span style="white-space:pre" class=""> </span>804<span style="white-space:pre" class=""> </span>Pfam<span style="white-space:pre" class=""> </span>PF17751<span style="white-space:pre" class=""> </span>SKICH domain<span style="white-space:pre" class=""> </span>555<span style="white-space:pre" class=""> </span>649<span style="white-space:pre" class=""> </span>9.8E-23<span style="white-space:pre" class=""> </span>T<span style="white-space:pre" class=""> </span>18-04-2019<span style="white-space:pre" class=""> </span>IPR041611<span style="white-space:pre" class=""> </span>SKICH domain</div><div class=""><br class=""></div><div class="">> map_data_ids genome.all.map output.renamed.iprscan</div><div class="">WARNING: No mapping available for ThuMac01937-RA</div><div class="">WARNING: No mapping available for ThuMac02226-RA</div><div class="">WARNING: No mapping available for ThuMac20730-RA</div><div class="">WARNING: No mapping available for ThuMac20730-RA</div><div class="">WARNING: No mapping available for ThuMac14750-RA</div><div class="">(Thousands of warnings like these were returned)</div><div class=""><br class=""></div><div class="">> maker_functional_gff uniprot_sprot.db output.renamed.blastp genome.all.renamed.gff > genome.all.renamed.putative_function.gff</div><div class="">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 class=""><br class=""></div><div class="">> head genome.all.renamed.putative_function.gff</div><div class="">##gff-version 3</div><div class="">scf7180000008677_pilon_pilon<span style="white-space:pre" class=""> </span>.<span style="white-space:pre" class=""> </span>contig<span style="white-space:pre" class=""> </span>1<span style="white-space:pre" class=""> </span>49996<span style="white-space:pre" class=""> </span>.<span style="white-space:pre" class=""> </span>.<span style="white-space:pre" class=""> </span>.<span style="white-space:pre" class=""> </span>ID=scf7180000008677_pilon_pilon;Name=scf7180000008677_pilon_pilon</div></div><div class=""><br class=""></div><div class="">Thanks in Advance,</div><div class=""><br class=""></div><div class="">Paul Sheridan</div><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class="">CSO at Tupac Bio<div class=""><a href="mailto:paul@tupac.bio" class="">Email: paul@tupac.bio</a></div><div class="">Homepage: <a href="http://www.paulsheridan.net/" target="_blank" class="">www.paulsheridan.net</a></div><div class="">Mobile: +81 80 7889 0859</div></div></div></div></div>
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