<div dir="ltr">Hi Carson,<div><br></div><div>Thanks, your suggestions got me sorted out.</div><div><br></div><div>Best,</div><div><br></div><div>Paul</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 23, 2019 at 2:50 AM Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">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><br></div><div>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><br></div><div><br></div><div>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><br></div><div>—Carson</div><div> </div><div><br><div><br><blockquote type="cite"><div>On Apr 18, 2019, at 3:23 AM, Paul Sheridan <<a href="mailto:paul@tupac.bio" target="_blank">paul@tupac.bio</a>> wrote:</div><br class="gmail-m_1264832190438329533Apple-interchange-newline"><div><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-wrap"> </span>P20036<span style="white-space:pre-wrap"> </span>41.791<span style="white-space:pre-wrap"> </span>134<span style="white-space:pre-wrap"> </span>77<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>326<span style="white-space:pre-wrap"> </span>458<span style="white-space:pre-wrap"> </span>113<span style="white-space:pre-wrap"> </span>246<span style="white-space:pre-wrap"> </span>9.51e-28<span style="white-space:pre-wrap"> </span>114</div><div>ThuMac19623-RA<span style="white-space:pre-wrap"> </span>P81018<span style="white-space:pre-wrap"> </span>35.714<span style="white-space:pre-wrap"> </span>168<span style="white-space:pre-wrap"> </span>87<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>147<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>168<span style="white-space:pre-wrap"> </span>8.40e-33<span style="white-space:pre-wrap"> </span>117</div><div>ThuMac19629-RA<span style="white-space:pre-wrap"> </span>Q66I51<span style="white-space:pre-wrap"> </span>68.939<span style="white-space:pre-wrap"> </span>264<span style="white-space:pre-wrap"> </span>79<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>263<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>262<span style="white-space:pre-wrap"> </span>1.48e-130<span style="white-space:pre-wrap"> </span>372</div><div>ThuMac19628-RA<span style="white-space:pre-wrap"> </span>Q61464<span style="white-space:pre-wrap"> </span>55.172<span style="white-space:pre-wrap"> </span>87<span style="white-space:pre-wrap"> </span>37<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>766<span style="white-space:pre-wrap"> </span>852<span style="white-space:pre-wrap"> </span>382<span style="white-space:pre-wrap"> </span>466<span style="white-space:pre-wrap"> </span>4.42e-25<span style="white-space:pre-wrap"> </span>119</div><div>ThuMac19627-RA<span style="white-space:pre-wrap"> </span>P07898<span style="white-space:pre-wrap"> </span>48.276<span style="white-space:pre-wrap"> </span>58<span style="white-space:pre-wrap"> </span>29<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>13<span style="white-space:pre-wrap"> </span>69<span style="white-space:pre-wrap"> </span>1962<span style="white-space:pre-wrap"> </span>2019<span style="white-space:pre-wrap"> </span>3.60e-13<span style="white-space:pre-wrap"> </span>65.9</div><div>ThuMac19626-RA<span style="white-space:pre-wrap"> </span>P81018<span style="white-space:pre-wrap"> </span>36.782<span style="white-space:pre-wrap"> </span>174<span style="white-space:pre-wrap"> </span>96<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>21<span style="white-space:pre-wrap"> </span>180<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>174<span style="white-space:pre-wrap"> </span>5.75e-36<span style="white-space:pre-wrap"> </span>127</div><div>ThuMac19624-RA<span style="white-space:pre-wrap"> </span>P81018<span style="white-space:pre-wrap"> </span>35.057<span style="white-space:pre-wrap"> </span>174<span style="white-space:pre-wrap"> </span>99<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>21<span style="white-space:pre-wrap"> </span>180<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>174<span style="white-space:pre-wrap"> </span>2.19e-33<span style="white-space:pre-wrap"> </span>120</div><div>ThuMac19625-RA<span style="white-space:pre-wrap"> </span>Q28343<span style="white-space:pre-wrap"> </span>32.520<span style="white-space:pre-wrap"> </span>123<span style="white-space:pre-wrap"> </span>43<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>35<span style="white-space:pre-wrap"> </span>117<span style="white-space:pre-wrap"> </span>2123<span style="white-space:pre-wrap"> </span>2245<span style="white-space:pre-wrap"> </span>7.57e-17<span style="white-space:pre-wrap"> </span>78.6</div><div>ThuMac19636-RA<span style="white-space:pre-wrap"> </span>Q9QX29<span style="white-space:pre-wrap"> </span>90.909<span style="white-space:pre-wrap"> </span>110<span style="white-space:pre-wrap"> </span>10<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>5<span style="white-space:pre-wrap"> </span>114<span style="white-space:pre-wrap"> </span>458<span style="white-space:pre-wrap"> </span>567<span style="white-space:pre-wrap"> </span>6.45e-65<span style="white-space:pre-wrap"> </span>216</div><div>ThuMac19638-RA<span style="white-space:pre-wrap"> </span>Q9QX29<span style="white-space:pre-wrap"> </span>57.391<span style="white-space:pre-wrap"> </span>115<span style="white-space:pre-wrap"> </span>35<span style="white-space:pre-wrap"> </span>3<span style="white-space:pre-wrap"> </span>5<span style="white-space:pre-wrap"> </span>114<span style="white-space:pre-wrap"> </span>703<span style="white-space:pre-wrap"> </span>808<span style="white-space:pre-wrap"> </span>3.06e-28<span style="white-space:pre-wrap"> </span>120</div><div><br></div><div>> head output.renamed.iprscan </div><div>ThuMac08407-RA<span style="white-space:pre-wrap"> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre-wrap"> </span>631<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF00520<span style="white-space:pre-wrap"> </span>Ion transport protein<span style="white-space:pre-wrap"> </span>154<span style="white-space:pre-wrap"> </span>413<span style="white-space:pre-wrap"> </span>3.8E-21<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR005821<span style="white-space:pre-wrap"> </span>Ion transport domain<span style="white-space:pre-wrap"> </span>GO:0005216|GO:0006811|GO:0016020|GO:0055085</div><div>ThuMac08407-RA<span style="white-space:pre-wrap"> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre-wrap"> </span>631<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF08412<span style="white-space:pre-wrap"> </span>Ion transport protein N-terminal<span style="white-space:pre-wrap"> </span>109<span style="white-space:pre-wrap"> </span>152<span style="white-space:pre-wrap"> </span>5.1E-19<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR013621<span style="white-space:pre-wrap"> </span>Ion transport N-terminal<span style="white-space:pre-wrap"> </span>Reactome: R-HSA-1296061</div><div>ThuMac08407-RA<span style="white-space:pre-wrap"> </span>f1e60af0e3add9ce493bd7a78114da1e<span style="white-space:pre-wrap"> </span>631<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF00027<span style="white-space:pre-wrap"> </span>Cyclic nucleotide-binding domain<span style="white-space:pre-wrap"> </span>519<span style="white-space:pre-wrap"> </span>601<span style="white-space:pre-wrap"> </span>1.0E-17<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR000595<span style="white-space:pre-wrap"> </span>Cyclic nucleotide-binding domain</div><div>ThuMac24094-RA<span style="white-space:pre-wrap"> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre-wrap"> </span>414<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF13765<span style="white-space:pre-wrap"> </span>SPRY-associated domain<span style="white-space:pre-wrap"> </span>235<span style="white-space:pre-wrap"> </span>283<span style="white-space:pre-wrap"> </span>8.9E-23<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR006574<span style="white-space:pre-wrap"> </span>SPRY-associated</div><div>ThuMac24094-RA<span style="white-space:pre-wrap"> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre-wrap"> </span>414<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF00643<span style="white-space:pre-wrap"> </span>B-box zinc finger<span style="white-space:pre-wrap"> </span>18<span style="white-space:pre-wrap"> </span>56<span style="white-space:pre-wrap"> </span>5.2E-12<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR000315<span style="white-space:pre-wrap"> </span>B-box-type zinc finger<span style="white-space:pre-wrap"> </span>GO:0008270</div><div>ThuMac24094-RA<span style="white-space:pre-wrap"> </span>f3c3ae9be61177558ac12f745bd0dd8e<span style="white-space:pre-wrap"> </span>414<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF00622<span style="white-space:pre-wrap"> </span>SPRY domain<span style="white-space:pre-wrap"> </span>287<span style="white-space:pre-wrap"> </span>391<span style="white-space:pre-wrap"> </span>2.2E-14<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR003877<span style="white-space:pre-wrap"> </span>SPRY domain<span style="white-space:pre-wrap"> </span>GO:0005515</div><div>ThuMac08369-RA<span style="white-space:pre-wrap"> </span>7aee1da5a47975ab8e43b68bfd1a117c<span style="white-space:pre-wrap"> </span>139<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF00076<span style="white-space:pre-wrap"> </span>RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)<span style="white-space:pre-wrap"> </span>22<span style="white-space:pre-wrap"> </span>87<span style="white-space:pre-wrap"> </span>1.6E-15<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR000504<span style="white-space:pre-wrap"> </span>RNA recognition motif domain<span style="white-space:pre-wrap"> </span>GO:0003676</div><div>ThuMac26054-RA<span style="white-space:pre-wrap"> </span>8f4119609312bd6442f8bb094c104231<span style="white-space:pre-wrap"> </span>462<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF07565<span style="white-space:pre-wrap"> </span>Band 3 cytoplasmic domain<span style="white-space:pre-wrap"> </span>173<span style="white-space:pre-wrap"> </span>443<span style="white-space:pre-wrap"> </span>7.3E-100<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR013769<span style="white-space:pre-wrap"> </span>Band 3 cytoplasmic domain<span style="white-space:pre-wrap"> </span>GO:0006820|GO:0008509|GO:0016021<span style="white-space:pre-wrap"> </span>Reactome: R-HSA-425381</div><div>ThuMac07958-RA<span style="white-space:pre-wrap"> </span>d2b749fa573a5e452cadee56090c9588<span style="white-space:pre-wrap"> </span>804<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF03372<span style="white-space:pre-wrap"> </span>Endonuclease/Exonuclease/phosphatase family<span style="white-space:pre-wrap"> </span>235<span style="white-space:pre-wrap"> </span>535<span style="white-space:pre-wrap"> </span>7.0E-11<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR005135<span style="white-space:pre-wrap"> </span>Endonuclease/exonuclease/phosphatase</div><div>ThuMac07958-RA<span style="white-space:pre-wrap"> </span>d2b749fa573a5e452cadee56090c9588<span style="white-space:pre-wrap"> </span>804<span style="white-space:pre-wrap"> </span>Pfam<span style="white-space:pre-wrap"> </span>PF17751<span style="white-space:pre-wrap"> </span>SKICH domain<span style="white-space:pre-wrap"> </span>555<span style="white-space:pre-wrap"> </span>649<span style="white-space:pre-wrap"> </span>9.8E-23<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>18-04-2019<span style="white-space:pre-wrap"> </span>IPR041611<span style="white-space:pre-wrap"> </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-wrap"> </span>.<span style="white-space:pre-wrap"> </span>contig<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>49996<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </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-m_1264832190438329533gmail_signature"><div dir="ltr">CSO at Tupac Bio<div><a href="mailto:paul@tupac.bio" target="_blank">Email: paul@tupac.bio</a></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>
_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><br></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><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>