Not Preprocessing for some reason

[Biomicrogen]

Program has been working great than all of a sudden I am getting this? Can't figure out why. I've been running with a set of manually entered kmer values and now I'm trying to run this with an auto selected value (without entering a -k option). Is there something I need to reset?

Initial command:

sudo ./initPipeline -q -1 /media/biomicrogen/U-Store-2/Processed-Seq/MiSEQ-270-PE1.fastq -2 /media/biomicrogen/U-Store-2/Processed-Seq/MiSEQ-270-PE2.fastq -c /media/biomicrogen/UBDISK/biomicrogen/BP-Trinity.fasta -d /media/biomicrogen/UBDISK/biomicrogen/runs/270-Trin -i 300:700 -W iMetAMOS

Run Command: sudo ./runPipeline -d /media/biomicrogen/UBDISK/biomicrogen/runs/Raw-Trin -v -o 40 -p 8 -f Scaffold -n Classify

Oops, MetAMOS finished with errors! see text in red above for details. Traceback (most recent call last): File "./runPipeline", line 985, in verbose = 1) File "/media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/ruffus/task.py", line 2965, in pipeline_run raise job_errors RethrownJobError:

Exception #1
  'exceptions.IOError([Errno 2] No such file or directory: '/media/biomicrogen/UBDISK/biomicrogen/runs/Raw-Trin/Assemble/out/proba.kmer')' raised in ...
   Task = def assemble.SplitAssemblers(...):
   Job  = [preprocess.success -> *.run]

Traceback (most recent call last):
  File "/media/biomicrogen/UBDISK/biomicrogen/metamos/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 "/media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/ruffus/task.py", line 491, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/media/biomicrogen/UBDISK/biomicrogen/metamos/src/assemble.py", line 293, in SplitAssemblers
    stats = open("%s/Assemble/out/%s.kmer"%(_settings.rundir, _settings.PREFIX), 'w')
IOError: [Errno 2] No such file or directory: '/media/biomicrogen/UBDISK/biomicrogen/runs/Raw-Trin/Assemble/out/proba.kmer'

[skoren]

Hi,

When you let metAMOS auto-set a k-mer it relies on KmerGenie which has some dependences metAMOS doesn't install (R and required packages). I think there is a bug in the code where if it cannot run kmergenie it will give the error you are seeing rather than defaulting to k=31. Can you check the ASSEMBLE.log for error messages? There should also be a command to run KmerGenie in COMMANDS.log.

[skoren]

Closing, inactivity.