mikecroucher / bcbio_examples Goto Github PK

Traceback (most recent call last):
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a//tools/bin/bcbio_nextgen.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.6a0', 'bcbio_nextgen.py')
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/setuptools-19.1.1-py2.7.egg/pkg_resources/__init__.py", line 745, in run_script

  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/setuptools-19.1.1-py2.7.egg/pkg_resources/__init__.py", line 1670, in run_script

  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.6a0-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in <module>
    main(**kwargs)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.6a0-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
    run_main(**kwargs)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 39, in run_main
    fc_dir, run_info_yaml)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 240, in rnaseqpipeline
    samples = run_parallel("process_alignment", samples)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 804, in __call__
    while self.dispatch_one_batch(iterator):
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 662, in dispatch_one_batch
    self._dispatch(tasks)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 570, in _dispatch
    job = ImmediateComputeBatch(batch)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 183, in __init__
    self.results = batch()
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
    return apply(f, *args, **kwargs)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 39, in process_alignment
    return sample.process_alignment(*args)
  File "/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 140, in process_alignment
    "If it is a fastq file (not pre-aligned BAM or CRAM), "
ValueError: Could not process input file from sample configuration. 
/fastdata/fe1mpc/sandeep/TDP_Omics_Study/Data/R1/CytTrc_Control/31-SHF7_141009_L004_R1.fastq.gz
Is the path to the file correct or is empty?
If it is a fastq file (not pre-aligned BAM or CRAM), is an aligner specified in the input configuration?