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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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Jan 2014 - Frozen Binary - run_test.sh error #102

Closed chrisdag closed 10 years ago

chrisdag commented 10 years ago

Latest frozen binary from mid-jan 2014 throwing this error when test/run_test_sh is run:

Starting Task = preprocess.PREPROCESS
    Job = [[carsonella_pe_filt.fna] -> preprocess.success] completed
Completed Task = preprocess.Preprocess
Starting Task = assemble.ASSEMBLE
    Job = [preprocess.success -> *.run] completed
Completed Task = assemble.SplitAssemblers
    Job = [soapdenovo.run -> soapdenovo.asm.contig] completed
Completed Task = assemble.Assemble
    Job = [[soapdenovo.asm.contig] -> [assemble.ok]] completed
Completed Task = assemble.CheckAsmResults
    Job = [[soapdenovo.asm.contig] -> *.asm.contig] completed
Completed Task = assemble.SplitMappers
Input is /metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/soapdenovo.asm.contig output /metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/soapdenovo.contig.cvg

Starting Task = mapreads.MAPREADS
    Job = [soapdenovo.asm.contig -> soapdenovo.contig.cvg] completed
Completed Task = mapreads.MapReads
Starting Task = validate.VALIDATE
    Job = [[soapdenovo.contig.cvg] -> [proba.lap]] completed
Completed Task = validate.Validate
Starting Task = findorfs.FINDORFS
    Job = [proba.asm.contig -> proba.faa] completed
Completed Task = findorfs.FindORFS
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 /tmp/_MEIDjE9xG/Utilities/perl/ImportFCP.pl  -c -i -f /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.epsilon-nb_results.txt:/metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/proba.contig.cnt:class

*************************DETAILS***********************************
Last 10 commands run before the error (/metamos/frozen-binary/metAMOS_binary/Test/test1/Logs/COMMANDS.log)
|2014-01-19 12:21:59| /tmp/_MEIDjE9xG/Utilities/cpp/Linux-x86_64/blastn -query /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig_part1.fa -out  /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.bl_results.txt -db /metamos/frozen-binary/metAMOS_binary/DB//blastdbs//blast_data/BacteriaAndArchaeaGenomesDB -evalue 10 -outfmt 7 -task blastn -num_threads 24
|2014-01-19 12:22:00| /tmp/_MEIDjE9xG/Utilities/cpp/Linux-x86_64/NB-BL /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.nb_results.txt /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.bl_results.txt /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.epsilon-nb_results.txt
|2014-01-19 12:22:00| unlink /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.hits
|2014-01-19 12:22:00| unlink /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.nb_results.txt
|2014-01-19 12:22:00| unlink /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.bl_results.txt
|2014-01-19 12:22:00| ln /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.epsilon-nb_results.txt /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.hits
|2014-01-19 12:22:00| rm /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig_part1.fa
|2014-01-19 12:22:00| cat /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/*.intermediate.hits > /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.hits
|2014-01-19 12:22:00| cat /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/*.intermediate.epsilon-nb_results.txt | grep -v 'Fragment Id' > /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.epsilon-nb_results.txt
|2014-01-19 12:22:01| perl /tmp/_MEIDjE9xG/Utilities/perl/ImportFCP.pl  -c -i -f /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.epsilon-nb_results.txt:/metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/proba.contig.cnt:class

Last 10 lines of output (/metamos/frozen-binary/metAMOS_binary/Test/test1/Logs/ANNOTATE.log)
Building results file: .
Done.
Processing blastn results...
Processing NB results...
Calculating NB-BL scores...
Writing out results...
Done.
unlink: cannot unlink `/metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.hits': No such file or directory
Loading taxonomy...
Taxonomy not found in /metamos/frozen-binary/metAMOS_binary/DB//taxonomy.  Was updateTaxonomy.sh run? at /tmp/_MEIDjE9xG/KronaTools/lib/KronaTools.pm line 1029.

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.
*************************ERROR***********************************
*****************************************************************
rm: cannot remove `/metamos/frozen-binary/metAMOS_binary/Test/test1/Logs/annotate.ok': No such file or directory
ruffus.ruffus_exceptions.RethrownJobError: 

    Exceptions running jobs for

    'def annotate.Annotate(...):'

    Original exception:

    Exception #1
    exceptions.NameError(global name 'JobSignalledBreak' is not defined):
    for annotate.Annotate.Job = [proba.faa -> proba.hits]

    Traceback (most recent call last):
      File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/ruffus.task", line 517, in run_pooled_job_without_exceptions
      File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/ruffus.task", line 447, in job_wrapper_io_files
      File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/annotate", line 440, in Annotate
      File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/utils", line 873, in run_process
    NameError: global name 'JobSignalledBreak' is not defined
treangen commented 10 years ago

hi Chris,

Thanks for sending, this is a known issue related to the externalization of the Krona DB directory for the frozen binary. This issue should be resolved per the latest released frozen bin (September 2013), but will take another look to ensure the currently linked version includes the patch.

-Todd

Latest frozen binary from mid-jan 2014 throwing this error when test/run_test_sh is run:

|Starting Task = preprocess.PREPROCESS Job = [[carsonella_pe_filt.fna] -> preprocess.success] completed Completed Task = preprocess.Preprocess Starting Task = assemble.ASSEMBLE Job = [preprocess.success -> .run] completed Completed Task = assemble.SplitAssemblers Job = [soapdenovo.run -> soapdenovo.asm.contig] completed Completed Task = assemble.Assemble Job = [[soapdenovo.asm.contig] -> [assemble.ok]] completed Completed Task = assemble.CheckAsmResults Job = [[soapdenovo.asm.contig] -> .asm.contig] completed Completed Task = assemble.SplitMappers Input is /metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/soapdenovo.asm.contig output /metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/soapdenovo.contig.cvg

Starting Task = mapreads.MAPREADS Job = [soapdenovo.asm.contig -> soapdenovo.contig.cvg] completed Completed Task = mapreads.MapReads Starting Task = validate.VALIDATE Job = [[soapdenovo.contig.cvg] -> [proba.lap]] completed Completed Task = validate.Validate Starting Task = findorfs.FINDORFS Job = [proba.asm.contig -> proba.faa] completed Completed Task = findorfs.FindORFS 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 /tmp/_MEIDjE9xG/Utilities/perl/ImportFCP.pl -c -i -f /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.epsilon-nb_results.txt:/metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/proba.contig.cnt:class

****DETAILS****** Last 10 commands run before the error (/metamos/frozen-binary/metAMOS_binary/Test/test1/Logs/COMMANDS.log) |2014-01-19 12:21:59| /tmp/_MEIDjE9xG/Utilities/cpp/Linux-x86_64/blastn -query /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig_part1.fa -out /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.bl_results.txt -db /metamos/frozen-binary/metAMOS_binary/DB//blastdbs//blast_data/BacteriaAndArchaeaGenomesDB -evalue 10 -outfmt 7 -task blastn -num_threads 24 |2014-01-19 12:22:00| /tmp/_MEIDjE9xG/Utilities/cpp/Linux-x86_64/NB-BL /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.nb_results.txt /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.bl_results.txt /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.epsilon-nb_results.txt |2014-01-19 12:22:00| unlink /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.hits |2014-01-19 12:22:00| unlink /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.nb_results.txt |2014-01-19 12:22:00| unlink /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.bl_results.txt |2014-01-19 12:22:00| ln /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.epsilon-nb_results.txt /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.hits |2014-01-19 12:22:00| rm /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig_part1.fa |2014-01-19 12:22:00| cat /metamos/frozen-binary/metAMOSbinary/Test/test1/Annotate/out/.intermediate.hits > /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.hits |2014-01-19 12:22:00| cat /metamos/frozen-binary/metAMOSbinary/Test/test1/Annotate/out/.intermediate.epsilon-nb_results.txt | grep -v 'Fragment Id' > /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.epsilon-nb_results.txt |2014-01-19 12:22:01| perl /tmp/_MEIDjE9xG/Utilities/perl/ImportFCP.pl -c -i -f /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/in/proba.asm.contig /metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.epsilon-nb_results.txt:/metamos/frozen-binary/metAMOS_binary/Test/test1/Assemble/out/proba.contig.cnt:class

Last 10 lines of output (/metamos/frozen-binary/metAMOS_binary/Test/test1/Logs/ANNOTATE.log) Building results file: . Done. Processing blastn results... Processing NB results... Calculating NB-BL scores... Writing out results... Done. unlink: cannot unlink `/metamos/frozen-binary/metAMOS_binary/Test/test1/Annotate/out/proba.ctg_1.intermediate.hits': No such file or directory Loading taxonomy... Taxonomy not found in /metamos/frozen-binary/metAMOS_binary/DB//taxonomy. Was updateTaxonomy.sh run? at /tmp/_MEIDjE9xG/KronaTools/lib/KronaTools.pm line 1029.

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team. ****ERROR******

rm: cannot remove `/metamos/frozen-binary/metAMOS_binary/Test/test1/Logs/annotate.ok': No such file or directory ruffus.ruffus_exceptions.RethrownJobError:

 Exceptions running jobs for

 'def annotate.Annotate(...):'

 Original exception:

 Exception #1
 exceptions.NameError(global name 'JobSignalledBreak' is not defined):
 for annotate.Annotate.Job = [proba.faa -> proba.hits]

 Traceback (most recent call last):
   File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/ruffus.task", line 517, in run_pooled_job_without_exceptions
   File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/ruffus.task", line 447, in job_wrapper_io_files
   File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/annotate", line 440, in Annotate
   File "/cbcb/project-scratch/treangen/metAMOS_tip/build/pyi.linux2/MA/out00-PYZ.pyz/utils", line 873, in run_process
 NameError: global name 'JobSignalledBreak' is not defined

— Reply to this email directly or view it on GitHub https://github.com/treangen/metAMOS/issues/102.

skoren commented 10 years ago

Closing as should be fixed in 1.5rc1. To resolve, you will have to restore the taxonomy directory by downloading the DBs again. You can download just the mini DB and copy its taxonomy to your existing database directory. Once this is done, release 1.5rc1 should no longer remove the taxonomy directory after running. Please reopen if you encounter this issue again.