Help Debugging Failed run

[coflynn]

Hello,

I can't work out how to fix the following problem. I have carried out my own assembly and therefore want to skip that step.

i start the pipeline with

../initPipeline -1 Pool1_sample1_R1.PF.fastq -2 Pool1_sample1_R2.PF.fastq -c Contigs-500.txt -d rawread-realcont -f -i 200:680 1> wed.o 2> wed.e &

works ok ..

Project dir /data/oflyncia/sample_metAmos/rawread-realcont successfully created! Use runPipeline.py to start Pipeline

so I do;

runPipeline -d rawread-realcont/ -c phylosift -a sparseassembler -o 25 -k 51 -p 1 -v -n "Assemble" 1> wed2.o 2> wed2.e &

But then something goes wrong...

I get the following error

Job = [[Pool1_sample1_R1.PF.fastq, Pool1_sample1_R2.PF.fastq] -> preprocess.success] completed Completed Task = preprocess.Preprocess Job = [[lib1.seq] -> [proba.asm.contig]] completed Completed Task = assemble.Assemble Traceback (most recent call last): File "/data/metAMOS/runPipeline", line 366, in pipeline_run([preprocess.Preprocess,assemble.Assemble,findorfs.FindORFS, findreps.FindRepeats, annotate.Annotate, abundance.Abundance , scaffold.Scaffold, findscforfs.FindScaffoldORFS, propagate.Propagate, classify.Classify, postprocess.Postprocess], verbose = 1) File "/data//metAMOS/Utilities/ruffus/task.py", line 2680, in pipeline_run raise errt ruffus.ruffus_exceptions.RethrownJobError:

Exceptions running jobs for

'def mapreads.MapReads(...):'

Original exception:

Exception #1
exceptions.KeyError('DBRH'):
for mapreads.MapReads.Job = [proba.asm.contig -> proba.bout]

Traceback (most recent call last):
  File "/data/metAMOS/Utilities/ruffus/task.py", line 524, in run_pooled_job_without_exceptions
    return t_job_result(task_name, JOB_COMPLETED, job_name, return_value, None)
  File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
    self.gen.throw(type, value, traceback)
  File "/data/metAMOS/Utilities/ruffus/task.py", line 232, in do_nothing_semaphore
    yield
  File "/data/metAMOS/Utilities/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
  File "/data/metAMOS/Utilities/ruffus/task.py", line 447, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/data/metAMOS/src/mapreads.py", line 350, in MapReads
    map2contig()
  File "/data/metAMOS/src/mapreads.py", line 254, in map2contig
    libcov_dict[ref][read[3][0:4]][read[0]+ii] = 1
KeyError: 'DBRH'

and then in the project folder i have

PREPROCESS.log

rm: cannot remove `/data/oflyncia/sample_matAmos/rawread-realcont/Preprocess/out/all.seq.mates': No such file or directory

SCAFFOLD.log

Which looks pretty normal.

Any Idea? thanks in advance