Rakefile issue

[kbrevs]

Hey, this seems similar to another recent issue (involving the bio gem not being installed), but I am running into this issue now, and I am unsure what the error is indicating - if it is an issue with my gff or with ruby. Here is the trace, followed by the first three lines of my .gff.

rake --trace [ 3:01PM] Invoke default (first_time) Execute default ** Invoke run/liftover.chn (first_time, not_needed) mkdir lepdec_OGSv1.0_ONLY_GENES.gff-liftover-Ldec_redundans_on_alpaths_contigs_genome liftOver -gff lepdec_OGSv1.0_ONLY_GENES.gff run/liftover.chn lepdec_OGSv1.0_ONLY_GENES.gff-liftover-Ldec_redundans_on_alpaths_contigs_genome/lifted.gff3 lepdec_OGSv1.0_ONLY_GENES.gff-liftover-Ldec_redundans_on_alpaths_contigs_genome/unlifted.gff3 Reading liftover chains Mapping coordinates WARNING: -gff is not recommended. Use 'ldHgGene -out=' and then 'liftOver -genePred ' /var/lib/gems/2.2.0/gems/bio-1.5.1/lib/bio/db/gff.rb:921: warning: regexp match /.../n against to UTF-8 string rake aborted! undefined method last' for nil:NilClass /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:72:inblock in process_gff' /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:69:in each' /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:69:ingroup_by' /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:69:in process_gff' /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:223:inblock (2 levels) in <top (required)>' /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:212:in each' /home/beetle/Documents/CPB/reference_genomes/flo/Rakefile:212:inblock in <top (required)>' /usr/lib/ruby/vendor_ruby/rake/task.rb:246:in call' /usr/lib/ruby/vendor_ruby/rake/task.rb:246:inblock in execute' /usr/lib/ruby/vendor_ruby/rake/task.rb:241:in each' /usr/lib/ruby/vendor_ruby/rake/task.rb:241:inexecute' /usr/lib/ruby/vendor_ruby/rake/task.rb:184:in block in invoke_with_call_chain' /usr/lib/ruby/2.2.0/monitor.rb:211:inmon_synchronize' /usr/lib/ruby/vendor_ruby/rake/task.rb:177:in invoke_with_call_chain' /usr/lib/ruby/vendor_ruby/rake/task.rb:170:ininvoke' /usr/lib/ruby/vendor_ruby/rake/application.rb:143:in invoke_task' /usr/lib/ruby/vendor_ruby/rake/application.rb:101:inblock (2 levels) in top_level' /usr/lib/ruby/vendor_ruby/rake/application.rb:101:in each' /usr/lib/ruby/vendor_ruby/rake/application.rb:101:inblock in top_level' /usr/lib/ruby/vendor_ruby/rake/application.rb:110:in run_with_threads' /usr/lib/ruby/vendor_ruby/rake/application.rb:95:intop_level' /usr/lib/ruby/vendor_ruby/rake/application.rb:73:in block in run' /usr/lib/ruby/vendor_ruby/rake/application.rb:160:instandard_exception_handling' /usr/lib/ruby/vendor_ruby/rake/application.rb:70:in run' /usr/bin/rake:27:in

' Tasks: TOP => default

GFF: Scaffold1 OGSv1.0 gene 12481 16948 . - . ID=LDEC000001;Name=LDEC000001;Dbxref=I5KNAL:LDEC000001;method=Maker Scaffold1 OGSv1.0 gene 19920 23242 . - . ID=LDEC000002;Name=LDEC000002;Dbxref=I5KNAL:LDEC000002;method=Maker Scaffold1 OGSv1.0 gene 26074 37602 . + . ID=LDEC000003;Name=LDEC000003;Dbxref=I5KNAL:LDEC000003;method=Maker

Thanks! Kristian

[yeban]

Hey. I made some changes to flo to address this. Do you think you can test it?

[kbrevs]

Great, thank you! I just ran it, and got new error messages: rake --trace [ 9:34AM] Invoke default (first_time) Execute default Invoke run/liftover.chn (first_time) Execute run/liftover.chn mkdir run cp Ldec.genome.10062013.fa run/source.fa cp Ldec_redundans_on_alpaths_contigsgenome.fa run/target.fa faToTwoBit run/source.fa run/source.2bit faToTwoBit run/target.fa run/target.2bit twoBitInfo run/source.2bit stdout | sort -k2nr > run/source.sizes twoBitInfo run/target.2bit stdout | sort -k2nr > run/target.sizes faSplit sequence run/target.fa 20 run/chunk rake aborted! Command failed with status (127): [faSplit sequence run/target.fa 20 run/chun...] /usr/lib/ruby/vendor_ruby/rake/file_utils.rb:53:in block in create_shell_runner' /usr/lib/ruby/vendor_ruby/rake/file_utils.rb:45:incall' /usr/lib/ruby/vendor_ruby/rake/file_utils.rb:45:in sh' /usr/lib/ruby/vendor_ruby/rake/file_utils_ext.rb:37:insh' /home/beetle/Documents/CPB/reference_genomes/flov2/flo/Rakefile:175:in block in <top (required)>' /usr/lib/ruby/vendor_ruby/rake/task.rb:246:incall' /usr/lib/ruby/vendor_ruby/rake/task.rb:246:in block in execute' /usr/lib/ruby/vendor_ruby/rake/task.rb:241:ineach' /usr/lib/ruby/vendor_ruby/rake/task.rb:241:in execute' /usr/lib/ruby/vendor_ruby/rake/task.rb:184:inblock in invoke_with_call_chain' /usr/lib/ruby/2.2.0/monitor.rb:211:in mon_synchronize' /usr/lib/ruby/vendor_ruby/rake/task.rb:177:ininvoke_with_call_chain' /usr/lib/ruby/vendor_ruby/rake/task.rb:170:in invoke' /home/beetle/Documents/CPB/reference_genomes/flov2/flo/Rakefile:222:inblock in <top (required)>' /usr/lib/ruby/vendor_ruby/rake/task.rb:246:in call' /usr/lib/ruby/vendor_ruby/rake/task.rb:246:inblock in execute' /usr/lib/ruby/vendor_ruby/rake/task.rb:241:in each' /usr/lib/ruby/vendor_ruby/rake/task.rb:241:inexecute' /usr/lib/ruby/vendor_ruby/rake/task.rb:184:in block in invoke_with_call_chain' /usr/lib/ruby/2.2.0/monitor.rb:211:inmon_synchronize' /usr/lib/ruby/vendor_ruby/rake/task.rb:177:in invoke_with_call_chain' /usr/lib/ruby/vendor_ruby/rake/task.rb:170:ininvoke' /usr/lib/ruby/vendor_ruby/rake/application.rb:143:in invoke_task' /usr/lib/ruby/vendor_ruby/rake/application.rb:101:inblock (2 levels) in top_level' /usr/lib/ruby/vendor_ruby/rake/application.rb:101:in each' /usr/lib/ruby/vendor_ruby/rake/application.rb:101:inblock in top_level' /usr/lib/ruby/vendor_ruby/rake/application.rb:110:in run_with_threads' /usr/lib/ruby/vendor_ruby/rake/application.rb:95:intop_level' /usr/lib/ruby/vendor_ruby/rake/application.rb:73:in block in run' /usr/lib/ruby/vendor_ruby/rake/application.rb:160:instandard_exception_handling' /usr/lib/ruby/vendor_ruby/rake/application.rb:70:in run' /usr/bin/rake:27:in

' Tasks: TOP => run/liftover.chn

I failed to add that I was able to run it successfully on a different gff (which I later realized was an outdated annotation set. It looks like the formatted isn't preserved by github, but here are the first few lines of the gff which did run to completion (I wasn't able to discern a formatting difference):

Scaffold1 WebApollo gene 1790498 1794021 . + . Name=916B82F966EEA6552CB9A3AFD9F1B307;date_creation=2014-07-21;owner=spalli;ID=916B82F966EEA6552CB9A3AFD9F1B307;date_last_modified=2014-09-24 Scaffold1 WebApollo mRNA 1790498 1794021 . + . Name=conserved oligomeric golgi complex subunit 1 ;date_creation=2014-07-21;Parent=916B82F966EEA6552CB9A3AFD9F1B307;symbol=IdICP;description=ExScaffold1 WebApollo exon 1790660 1790887 . + . Name=0C0A7D3097A5D5F597D2E77A89F9FAB5;date_creation=2014-07-21;Parent=62272803AB84FD406888F0C4BC209A78;owner=spalli;ID=0C0A7D3097A5D5F597D2E77A

Thanks!

[yeban]

I think this new error is unrelated and is caused by somehow flo not being able to find faSplit command.

[kbrevs]

Yes, you are correct - a migration issue. Teach me to do things so early on a Monday. :) Looks like it is running perfect now. Thanks!