<div dir="ltr"><div>I completed the first round of Maker. I subsequently trained Snap, Genemark-es, and Augustus. I've since fed those results back into Maker for a second round. Some sequences were successful, others were not. On some, I encountered an error about calling translate without a seq argument. I read some other threads about similar issues, and I followed the advice to isolate a single sequence using -g and -base. My config files can be found at this link: <a href="https://byu.box.com/s/1tbp48djblo31ruuy8zm62k1vxoyozhq">https://byu.box.com/s/1tbp48djblo31ruuy8zm62k1vxoyozhq</a>. <br></div><div><br></div><div>The following are the contents of stderr:</div><div><br></div><div style="margin-left:40px"><span style="color:rgb(56,118,29)"><span style="font-family:monospace">STATUS: Parsing control files...<br>STATUS: Processing and indexing input FASTA files...<br>STATUS: Setting up database for any GFF3 input...<br>A data structure will be created for you at:<br>/path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore<br><br>To access files for individual sequences use the datastore index:<br>/path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_master_datastore_index.log<br><br>STATUS: Now running MAKER...<br>examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: scaffold_66<br>Length: 2264627<br>#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br>collecting blastx repeatmasking<br>processing all repeats<br>in cluster::shadow_cluster...<br>...finished clustering.<br>doing repeat masking<br>collecting blastx repeatmasking<br>processing all repeats<br>in cluster::shadow_cluster...<br>...finished clustering.<br>preparing masked sequence<br>preparing ab-inits<br>running  snap.<br>#--------- command -------------#<br>Widget::snap:<br>/path/to/snap /path/to/data/snap/rnd1/genome.hmm /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0 > /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0.genome%2Ehmm.snap<br>#-------------------------------#<br>scoring....decoding.10.20.30.40.50.60.70.80.90.100 done<br>scoring....decoding.10.20.30.40.50.60.70.80.90.100 done<br>running  augustus.<br>#--------- command -------------#<br>Widget::augustus:<br>/path/to/apps/augustus/3.3.2/final/bin/augustus --AUGUSTUS_CONFIG_PATH=/path/to/data/augustus_config --species=pacbf --UTR=off /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0 > /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0.pacbf.augustus<br>#-------------------------------#<br>running  genemark.<br>#--------- command -------------#<br>Widget::genemark:<br>/path/to/apps/perl/5.28/perl/bin/perl /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Widget/genemark/gmhmm_wrap -m /path/to/data/gmes/output/gmhmm.mod -g /path/to/apps/genemark-es/4.38/gmhmme3 -p /path/to/apps/genemark-es/4.38/probuild -o /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_nomask.0.gmhmm%2Emod.genemark /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_nomask.0<br>#-------------------------------#<br>gathering ab-init output files<br>deleted:0 genes<br>deleted:0 genes<br>substr outside of string at /path/to/apps/perl/5.28/perl/lib/5.28.0/Carp.pm line 346.<br><br>------------- EXCEPTION: Bio::Root::Exception -------------<br>MSG: Calling translate without a seq argument!<br>STACK: Error::throw<br>STACK: Bio::Root::Root::throw /path/to/apps/bioperl/1.7.2/perl5/lib/perl5/Bio/Root/Root.pm:447<br>STACK: Bio::Tools::CodonTable::translate /path/to/apps/bioperl/1.7.2/perl5/lib/perl5/Bio/Tools/CodonTable.pm:419<br>STACK: CGL::TranslationMachine::longest_translation_plus_stop /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/CGL/TranslationMachine.pm:280<br>STACK: maker::auto_annotator::get_translation_seq /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/maker/<a href="http://auto_annotator.pm:3575">auto_annotator.pm:3575</a><br>STACK: Widget::snap::load_phat_hits /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Widget/<a href="http://snap.pm:973">snap.pm:973</a><br>STACK: Widget::snap::parse /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Widget/<a href="http://snap.pm:689">snap.pm:689</a><br>STACK: GI::parse_abinit_file /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/GI.pm:1228<br>STACK: Process::MpiChunk::_go /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiChunk.pm:1473<br>STACK: Process::MpiChunk::run /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiChunk.pm:340<br>STACK: Process::MpiChunk::run_all /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiChunk.pm:356<br>STACK: Process::MpiTiers::run_all /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiTiers.pm:287<br>STACK: Process::MpiTiers::run_all /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiTiers.pm:287<br>STACK: /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/maker:679<br>-----------------------------------------------------------<br>--> rank=NA, hostname=<a href="http://somenode.rc.byu.edu">somenode.rc.byu.edu</a><br>ERROR: Failed while gathering ab-init output files<br>ERROR: Chunk failed at level:1, tier_type:2<br>FAILED CONTIG:scaffold_66<br><br>ERROR: Chunk failed at level:4, tier_type:0<br>FAILED CONTIG:scaffold_66<br><br>examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>Processing run.log file...<br><br><br>Maker is now finished!!!</span></span></div><div><br></div><div>The command I ran was as follows:</div><div><br></div><div style="margin-left:40px"><span style="color:rgb(56,118,29)"><span style="font-family:monospace">maker -g /path/to/data/originalAssembly/split/scaffold_66.fasta \</span></span></div><div style="margin-left:40px"><span style="color:rgb(56,118,29)"><span style="font-family:monospace">    -base scaffolds -TMP /tmp/35082116 -cpus 1 </span></span><br></div><div><div><div data-smartmail="gmail_signature" class="gmail_signature" dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><br></div><div>I usually run maker with MPI (e.g., <span style="font-family:monospace">mpirun maker -TMP /tmp/abcdefg -cpus 1</span>), but didn't see any need when I was running a single sequence as a test. Note that this output from this isolated run matches what I've been seeing in the mixed output from MPI, just slightly jumbled together with other things.</div><div><br></div><div>The following is the bottom of the run.log file for this sequence in the datastore:</div><div><br></div><div style="margin-left:40px"><span style="color:rgb(56,118,29)"><span style="font-family:monospace">LOGCHILD    /path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/run.log.child.0<br>LOGCHILD    /path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/run.log.child.0<br>LOGCHILD    /path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/run.log.child.0<br>STARTED scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.genome%2Ehmm.snap<br>FINISHED    scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.genome%2Ehmm.snap<br>STARTED scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.pacbf.augustus<br>FINISHED    scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.pacbf.augustus<br>STARTED scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_nomask.0.gmhmm%2Emod.genemark<br>FINISHED    scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_nomask.0.gmhmm%2Emod.genemark<br>DIED    RANK    0:4:0:0<br>DIED    COUNT   1<br>DIED    RANK    0<br>DIED    COUNT   1</span></span></div><div><br></div><div>The contents of theVoid directory can be viewed at this link: <a href="https://byu.box.com/s/hqwngdvehs8dfoymtrkjyismq3p8ayv1">https://byu.box.com/s/hqwngdvehs8dfoymtrkjyismq3p8ayv1</a>.</div><div><br></div><div>Do you have any suggestions on how I can resolve this error? <br></div><div><br></div><div><font size="2">Thank you,</font></div><div><font size="2">Brandon</font><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>