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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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During findorfs, the following command failed with return code -6 #260

Open jtallman1 opened 7 years ago

jtallman1 commented 7 years ago

Hello,

When I try to run the program (at the runPipeline component), I get this error message at the "findorfs" step and I'm not sure what it means or what I should do to fix the issue:

*ERROR*** During findorfs, the following command failed with return code -6:

/home/apps/metAMOS/1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna -b /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna.bnk

*DETAILS*** Last 10 commands run before the error (/work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/Logs/COMMANDS.log) |2017-02-26 21:52:35| ln /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/Assemble/out/soapdenovo.31.asm.contig /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/in/soapdenovo.31.asm.contig |2017-02-26 22:04:51| /home/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/in/soapdenovo.31.asm.contig -o /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.orfs -w 0 -t complete |2017-02-26 22:04:53| mv /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.orfs.ffn /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.ctg.fna |2017-02-26 22:04:53| mv /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.orfs.faa /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.ctg.faa |2017-02-26 22:04:53| mv /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.gene.cvg /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.ctg.gene.cvg |2017-02-26 22:04:53| mv /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.gene.map /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.ctg.gene.map |2017-02-26 22:04:53| rm -r /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna |2017-02-26 22:04:54| cat /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31*.fna > /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna |2017-02-26 22:04:54| rm -r /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna.bnk |2017-02-26 22:17:12| /home/apps/metAMOS/1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna -b /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna.bnk

Last 10 lines of output (/work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/Logs/FINDORFS.log) no. of seqs: 496030 Read Bank doesn't exist; creating frag Bank doesn't exist; creating lib Bank doesn't exist; creating parsing fasta file terminate called after throwing an instance of 'AMOS::IOException_t' what(): Could not read bank, expected version: 3.0, saw version:

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

rm: cannot remove `/work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/Logs/findorfs.ok': No such file or directory Oops, MetAMOS finished with errors! see text in red above for details. Traceback (most recent call last): File "/home/apps/metAMOS/1.5rc3/runPipeline", line 991, in verbose = 1) File "/home/apps/metAMOS/1.5rc3/Utilities/ruffus/task.py", line 2965, in pipeline_run raise job_errors RethrownJobError: 

Exception #1
  'exceptions.TypeError(exceptions must be old-style classes or derived from BaseException, not NoneType)' raised in ...
   Task = def findorfs.FindORFS(...):
   Job  = [soapdenovo.31.contig.cvg -> soapdenovo.31.faa]

Traceback (most recent call last):
  File "/home/apps/metAMOS/1.5rc3/Utilities/ruffus/task.py", line 625, in run_pooled_job_without_exceptions
    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
  File "/home/apps/metAMOS/1.5rc3/Utilities/ruffus/task.py", line 491, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/home/apps/metAMOS/1.5rc3/src/findorfs.py", line 392, in FindORFS
    run_process(_settings, "%s/toAmos_new -s %s/FindORFS/out/%s.fna -b %s/FindORFS/out/%s.fna.bnk"%(_settings.AMOS, _settings.rundir, _settings.PREFIX, _settings.rundir, _settings.PREFIX), "FindORFS")
  File "/home/apps/metAMOS/1.5rc3/src/utils.py", line 1154, in run_process
    raise
TypeError: exceptions must be old-style classes or derived from BaseException, not NoneType

Thank you very much for your time! I greatly appreciate any help you can give me.

Thank you, James

skoren commented 7 years ago

Can you check what the size of the /work/VibrioGenome/jtallman1/Thesis/MetAMOS_Output2/FindORFS/out/soapdenovo.31.fna file is?

I suspect it is empty which is causing this issue.