[maker-devel] <MAKER Trac Server> #24: maker ignores fgenesh's segfault when given "too long" paths

[MAKER]

#24: maker ignores fgenesh's segfault when given "too long" paths
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 Reporter:  malcolm_cook at stowers-institute.org  |       Owner:       
     Type:  defect                              |      Status:  new  
 Priority:  major                               |   Milestone:       
Component:  Code                                |     Version:  0.001
 Keywords:                                      |  
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 fgenesh (version 2.4) will segfault apparently if the input path is "too
 long".

 maker does not raise any exception when this occurs

 paths produced by maker running maker's test/example can be "too long"
 depending on where the test directory is rooted.

 Steps to reproduce:

 with `maker` installed resulting in test directory at least a long as mine
 (namely /n/site/src/bioinfo/gmod/maker/test), run the test as:

 maker -f -predictor=fgenesh,snap,augustus maker_exe.ctl maker_opts.ctl
 maker_bopts.ctl 2> maker.log

 observe that
  1)  there are no fgenesh predictions in
 dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/contig-
 dpp-500-500.gff
  2) the fgenesh output files in the void are empty and the maker.log
 reports no error

 now mv the test directory to, say, your home directory and rerun maker as
 above, and observe that the gff output now holds fgenesh predictions.

 Also, confirming  if I just take the fgenesh command from the maker.log
 and directly re-execute it, I see segfault unless I move the files: i.e.

 mec at beta> fgenesh /n/site/inst/Linux-i686/bioinfo/fgenesh/current/db/Human
 /n/site/src/bioinfo/gmod/maker/test/dpp_contig.maker.output/dpp_contig_datastore
 /contig-dpp-500-500/theVoid.contig-
 dpp-500-500/0.auto_annotator.20907.fgenesh.fasta
 Segmentation fault
 mec at beta> cp
 /n/site/src/bioinfo/gmod/maker/test/dpp_contig.maker.output/dpp_contig_datastore
 /contig-dpp-500-500/theVoid.contig-
 dpp-500-500/0.auto_annotator.20907.fgenesh.fasta delme
 mec at beta> fgenesh /n/site/inst/Linux-i686/bioinfo/fgenesh/current/db/Human
 delme | head -n 1
  FGENESH 2.4 Prediction of potential genes in Homo_sapiens genomic DNA

-- 
Ticket URL: <http://malachite.genetics.utah.edu/projects/maker/ticket/24>
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