./run_pipeline_test.sh fails upon install from source

[fwhelan]

Good afternoon,

I get an error with MetAMOS upon installation from source (as outlined here http://metamos.readthedocs.org/en/v1.5rc3/content/installation.html#automated-installation).

...

Starting Task = assemble.ASSEMBLE
    Job  = [preprocess.success -> *.run] completed
Completed Task = assemble.SplitAssemblers
    Job  = [soapdenovo.55.run -> soapdenovo.55.asm.contig] completed
Completed Task = assemble.Assemble
    Job  = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed
Completed Task = assemble.CheckAsmResults
Uptodate Task = assemble.SplitMappers

Starting Task = mapreads.MAPREADS
    Job  = [soapdenovo.55.asm.contig -> soapdenovo.55.contig.cvg] completed
Completed Task = mapreads.MapReads
    Job  = [[soapdenovo.55.contig.cvg] -> [mapreads.ok]] completed
Completed Task = mapreads.CheckMapResults
Uptodate Task = mapreads.SplitForORFs
Starting Task = findorfs.FINDORFS
    Job  = [soapdenovo.55.contig.cvg -> soapdenovo.55.faa] completed
Completed Task = findorfs.FindORFS
Starting Task = validate.VALIDATE
    Job  = [[soapdenovo.55.faa] -> [validate.ok]] completed
Completed Task = validate.Validate
Starting Task = findrepeats.FINDREPEATS
    Job  = [proba.fna -> proba.repeats] completed
Completed Task = findreps.FindRepeats
Starting Task = annotate.ANNOTATE
*****************************************************************
*************************ERROR***********************************
During annotate, the following command failed with return code 2:
>> perl /home/fwhelan/software/metAMOS-1.5rc3/Utilities/perl/ImportKraken.pl  -c -i -f /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits:/home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt:class

*************************DETAILS***********************************
Last 10 commands run before the error (/home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Logs/COMMANDS.log)
|2014-10-22 15:10:38|# [ANNOTATE]
|2014-10-22 15:10:38| touch /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.annots
|2014-10-22 15:10:38| unlink /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig
|2014-10-22 15:10:38| ln /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig
|2014-10-22 15:10:38| unlink /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-10-22 15:10:38| rm -f /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.hits
|2014-10-22 15:10:38| rm -f /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.epsilon-nb_results.txt
|2014-10-22 15:10:38| rm -f /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.phymm.out
|2014-10-22 15:10:42| /home/fwhelan/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/fwhelan/software/metAMOS-1.5rc3/Utilities/DB//kraken /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig --preload   | kraken-filter --db /home/fwhelan/software/metAMOS-1.5rc3/Utilities/DB//kraken --threshold 0.05 > /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-10-22 15:10:42| perl /home/fwhelan/software/metAMOS-1.5rc3/Utilities/perl/ImportKraken.pl  -c -i -f /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig /home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits:/home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt:class

Last 10 lines of output (/home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Logs/ANNOTATE.log)
unlink: cannot unlink ‘/home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits’: No such file or directory
Loading database... complete.
3 sequences (0.16 Mbp) processed in 3.044s (0.1 Kseq/m, 3.15 Mbp/m).
  3 sequences classified (100.00%)
  0 sequences unclassified (0.00%)
Loading taxonomy...
Taxonomy not found.  Was updateTaxonomy.sh run? at /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/lib/KronaTools.pm line 1019.

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.
*************************ERROR***********************************
*****************************************************************
rm: cannot remove ‘/home/fwhelan/software/metAMOS-1.5rc3/Test/test1/Logs/annotate.ok’: No such file or directory
Oops, MetAMOS finished with errors! see text in red above for details.

I can't install the frozen binary because, when I do, I encounter issue #147. I removed the Kronatools directory and re-installed based on advice in issue #124.

x86_64 GNU/Linux

Any advice greatly appreciated!

[treangen]

Hello,

can you verify that the following file is present on your system?

/home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy.tab

[fwhelan]

Hi, thanks for your reply. I have /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy/taxonomy.tab but not /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy.tab

[treangen]

Thanks for confirming that the file is present.

Could you also provide the output the following commands:

which ktGetLibPath

and

ktGetLibPath

[fwhelan]

That must be the problem- which ktGetLibPath returns nothing. How do I resolve this?

[dumaatravaie]

First thing please try to check whether you have all these files in the directory ?

/home/fwhelan/software/metAMOS-1.5rc3/KronaTools/bin/

ktClassifyBLAST ktGetContigMagnitudes ktGetLibPath ktGetTaxIDFromGI ktImportAmphora ktImportBLAST ktImportDiskUsage ktImportEC ktImportFCP ktImportGalaxy ktImportMETAREP-BLAST ktImportMETAREP-EC ktImportMGRAST ktImportPHMMER ktImportPhymmBL ktImportRDP ktImportRDPComparison ktImportTaxonomy ktImportText ktImportXML

If not then i think you have the problem with the installation of Kronatools, and in that case you need to change your Kronatool version from the metAmos INSTALL.py script at line number 124

from kronaTools = "KronaTools-2.2" to kronaTools = "KronaTools-2.4"

Finally you rerun the metAmos INSTALL.py in your existing metAmos installation directory ....

//------------------------------------------------------------------------------------------------------------------------------ //__ If not, Try to check this folder

/home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy/

and please give the name of all the files present this directory ......

[treangen]

hi Fiona,

That must be the problem- which ktGetLibPath returns nothing. How do I resolve this?

This was just to confirm you do not have a Krona installation outside of MetAMOS. Your ktGetLibPath should be present at:

/home/fwhelan/software/metAMOS-1.5rc3/KronaTools/bin/ktGetLibPath 

MetAMOS knows about this path and found it, but it is unknown to your $PATH environment variable, explaining why it was not found with which.

This issue is proving difficult to debug as the error you are experiencing should only occur if the taxonomy.tab file is missing from /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy/.

Some additional information is required to get to the bottom of this:

1. Can you list the file permissions & size of your installed taxonomy.tab? As you have already confirmed taxonomy.tab is present, it is possible (although unlikely) that you do not have the necessary read permissions to open the file.

   ls -la /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy/taxonomy.tab

2. Please add the following print statement before line 1042 in /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/ lib/KronaTools.pm :

   sub loadTaxonomy                                                                                                                                                        
   {  
      print "$taxonomyDir/taxonomy.tab\n"; 
      open INFO, "<$taxonomyDir/taxonomy.tab" or die                                                                                                                  
   ...
   }

   Once added, rerun MetAMOS. This will clarify where ImportKraken is expecting the taxonomy.tab file to be located on disk, which should be /home/fwhelan/software/metAMOS-1.5rc3/KronaTools/taxonomy/.

Regarding @dumaatravaie's comment, while I agree it would be helpful to confirm you have a valid KronaTools install, the Import script you are running (ImportKraken.pl) is located at:

   /home/fwhelan/software/metAMOS-1.5rc3/Utilities/perl/ImportKraken.pl

But the ImportKraken.pl was found and it ran; it is returning an error as it is unable to locate/open/access your taxonomy.tab file; hopefully the previous two suggestions will help to elucidate why it is unable to locate/use the file.

-Todd

[fwhelan]

Thanks to both of you for your replies. Based on @dumaatravaie 's comment, I found I had issue #163. rm -r KronaTools/ wasn't enough, but I just finished a brand new install with the modification to INSTALL.py listed above and I was able to pass ./run_pipeline_test.sh, so I'll give it a go with my own data now. Thank you both for your help!