<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="">Hi Kevin,<div class=""><br class=""></div><div class="">About using AGAT (agat_convert_sp_gxf2gxf.pl), two reasons to get empty output files.</div><div class="">I) The feature types (3rd column) are not yet handled by AGAT. You can inform AGAT how to deal with it </div><div class="">See <a href="https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-the-feature-type-is-not-yet-taken-into-account" class="">https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-the-feature-type-is-not-yet-taken-into-account</a></div><div class="">II) The features are thrown by AGAT because child feature are missing <span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">(e.g. gene feature expect at least one transcript linked to it)</span>. See <a href="https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-child-features-are-not-provided" class="">https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-child-features-are-not-provided</a></div><div class=""><br class=""></div><div class="">I invite you to open an issue in the AGAT GitHub repository.</div><div class=""><br class=""></div><div class="">Once the file is parsed correctly you can use the script agat_sp_alignment_output_style.pl to turn level1 feature types (e.g. gene) and level2 feature types (e.g. mRNA) into match and match_part features respectively as it can be preferred by MAKER.</div><div class=""><br class=""></div><div class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div>Best regards,</div><div><br class="">Jacques Dainat, Ph.D.<br class=""><br class=""></div></div></div>
</div>
<div><br class=""><blockquote type="cite" class=""><div class="">On 22 Sep 2021, at 18:21, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I’d have to see the GFF, but in general you should organize sequence alignments as match/match_part features.<div class=""><br class=""></div><div class="">Here is n example from the GFF3 format specification:</div><div class=""><br class=""></div><div class=""><div class=""><font face="Courier" class="">ctg123 . cDNA_match 1200 9000 . . . ID=cDNA00001</font></div><div class=""><font face="Courier" class="">ctg123 . match_part 1200 3200 2.2e-30 + . ID=match00002;Parent=cDNA00001;Target=mjm1123.5 5 506;Gap=M301 D1499 M201</font></div><div class=""><font face="Courier" class="">ctg123 . match_part 7000 9000 7.4e-32 - . ID=match00003;Parent=cDNA00001;Target=mjm1123.3 1 502;Gap=M101 D1499 M401</font></div><div class=""><br class=""></div><div class="">Also make sure you are not inadvertently using GFF2 or GTF. They are not backwards compatible with GFF3.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 22, 2021, at 8:06 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" class="">kmkocot@ua.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thanks Carson,</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">I think I see the problem now. Here's what I'm getting:</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-----<br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">STATUS: Parsing control files...<div class="">STATUS: Processing and indexing input FASTA files...</div><div class="">STATUS: Setting up database for any GFF3 input...</div><div class="">A data structure will be created for you at:</div><div class="">/home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_datastore</div><div class=""><br class=""></div><div class="">To access files for individual sequences use the datastore index:</div><div class="">/home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_master_datastore_index.log</div><div class=""><br class=""></div><div class="">STATUS: Now running MAKER...</div><div class="">examining contents of the fasta file and run log</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">--Next Contig--</div><div class=""><br class=""></div><div class="">Processing run.log file...</div><div class="">#---------------------------------------------------------------------</div><div class="">Now retrying the contig!!</div><div class="">SeqID: PGA_scaffold0</div><div class="">Length: 141759199</div><div class="">Tries: 5!!</div><div class="">#---------------------------------------------------------------------</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">setting up GFF3 output and fasta chunks</div><div class="">prepare section files</div><div class="">Gathering GFF3 input into hits - chunk:0</div><div class="">ERROR: Non-unique top level ID for match.19561.56</div><div class="">While this is technically legal in GFF3, it usually</div><div class="">indicates a poorly fomatted GFF3 file (perhaps you</div><div class="">tried to merge two GFF3 files without accounting for</div><div class="">unique IDs). MAKER will not handle these correctly.</div><div class=""><br class=""></div><div class="">--> rank=NA, hostname=wirenia</div><div class="">ERROR: Failed while prepare section files</div><div class="">ERROR: Chunk failed at level:12, tier_type:3</div><div class="">FAILED CONTIG:PGA_scaffold0</div><div class=""><br class=""></div><div class="">ERROR: Chunk failed at level:4, tier_type:0</div><div class="">FAILED CONTIG:PGA_scaffold0</div><div class=""><br class=""></div><div class="">examining contents of the fasta file and run log</div><span class=""></span>-----</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">It looks like maker doesn't like the format of the exonerate gff3 I am using. I tried 'fixing' it with agat_convert_sp_gxf2gxf.pl, which seemed to work on my Braker output, but that just produced an empty gff3 file for both my exonerate and PASA gff3 files. Any advice on how to prepare exonerate or PASA gff3 files for Maker?<br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Thanks!</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Kevin<br class=""><hr tabindex="-1" style="display: inline-block; width: 2044.265625px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, September 20, 2021 8:06 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Kevin Kocot <<a href="mailto:kmkocot@ua.edu" class="">kmkocot@ua.edu</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><span class="Apple-converted-space"> </span><<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure</font><div class=""> </div></div><div dir="auto" class="">Hi Kevin,<div class=""><br class=""></div><div class="">The files are already being skipped because of previous failures. Can you increase the try count (-t on the command line) to something like 6, and send me the STDERR after it generates a new failure.</div><div class=""><br class=""></div><div class="">—Carson <br class=""><br class=""><div dir="ltr" class="">Sent from my iPhone</div><div dir="ltr" class=""><br class=""><blockquote type="cite" class="">On Sep 20, 2021, at 4:56 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" class="">kmkocot@ua.edu</a>> wrote:<br class=""><br class=""></blockquote></div><blockquote type="cite" class=""><div dir="ltr" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thanks Carson! I've uploaded that file here:</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log" id="LPlnk439129" class="">http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log</a><br class=""></div><div class=""><div class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""><hr tabindex="-1" style="display: inline-block; width: 2034.46875px;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Carson Holt<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, September 14, 2021 9:51 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Kevin Kocot<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure<div class=""><br class=""></div></div><div class="x_rps_346f"><div class="" style="word-wrap: break-word; line-break: after-white-space;">What I really need is the captured STDERR from the failed run.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 10, 2021, at 9:19 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank" rel="noopener noreferrer" class="">kmkocot@ua.edu</a>> wrote:</div><br class="x_x_Apple-interchange-newline"><div class=""><div class="x_x_WordSection1" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;">Hi Carson and all,</span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;"> </span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;">I ran Maker 3.01.03 on a chromosome-level mollusc genome assembly using some evidence I previously generated with Funannotate and BRAKER2, but Maker is not completing successfully. Every scaffold in the datastore_index.log file has both STARTED and FAILED statuses. I can't figure out where the problem lies, though. Running ./Build status indicates all the dependencies are there (I’m not using MPI). The run.log files just ends with "DIED RANK 0" and "DIED COUNT 3." Is there a way to tell which (if any) of the dependencies is misbehaving here (they all seem to run fine independently) or if my evidence .gff3 files are not correctly formatted?</span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;"> </span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;">I’ve uploaded a<span class=""><span class="x_x_Apple-converted-space"> </span>zipped sample output folder as well as my config files</span><span class="x_x_Apple-converted-space"> </span>and the datastore.log file here:<span class="x_x_Apple-converted-space"> </span><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/" target="_blank" rel="noopener noreferrer" class="" style="color: rgb(5, 99, 193); text-decoration: underline;">http://genomes.ua.edu/Kocot/2021-09-10_Maker/</a><span class=""></span></span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;">Any guidance on what might be the issue would be greatly appreciated.</span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;"> </span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;">Thanks!</span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="" style="font-size: 12pt;">Kevin</span></div><div class="" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </div><p class="x_x_MsoNormal" style="margin: 7.5pt 0in 0in; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;"><b class=""><span class="" style="font-size: 12pt; font-family: Helvetica, sans-serif; color: rgb(153, 0, 0);">Kevin M. Kocot<br class=""></span></b><span class="" style="font-size: 8pt; font-family: Helvetica, sans-serif;">he/him/his</span><b class=""><span class="" style="font-size: 12pt; font-family: Helvetica, sans-serif; color: rgb(153, 0, 0);"></span></b></p><p class="x_x_MsoNormal" style="margin: 0in 0in 7.5pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;"><span class="" style="font-size: 11.5pt; font-family: Helvetica, sans-serif;">Associate Professor & Curator of Invertebrates<br class="">Department of Biological Sciences & Alabama Museum of Natural History<br class=""></span><span class="" style="font-size: 10.5pt; font-family: Helvetica, sans-serif;"><a href="https://www.ua.edu/" target="_blank" rel="noopener noreferrer" class="" style="color: rgb(5, 99, 193); text-decoration: underline;"><span class="" style="color: maroon; text-decoration: none;">The University of Alabama</span></a> <br class="">307 Mary Harmon Bryant Hall<br class="">Box 870344<br class="">Tuscaloosa, AL 35487<br class="">phone <a href="tel:205-348-4052" target="_blank" rel="noopener noreferrer" class="" style="color: rgb(5, 99, 193); 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