falcon_erro

[fanyucai1]

1:i download falcon from https://downloads.pacbcloud.com/public/falcon/ named falcon-2017.06.28-18.01-py2.7-ucs4.tar.gz

2:when i run the fc_run.py in the process of "0-rawreads"

3:i find erro in the shell python2.7 -m falcon_kit.mains.report_pre_assembly --genome-length 0 --length-cutoff 3000 --db /public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/raw_reads.db --preads-fofn /public/land/Pacbio/yangshu/falcon_3000_3000/0-rawread s/preads/input_preads.fofn --out pre_assembly_stats.json

4:The file "input_preads.fofn" contains list of fasta ,but when i open open fasta file it looks like:

**(True, ('aaacaagattcgctactttttttaaaagatagtgaagtcatcgttccttgtaaaagttgtgtgatttgtgcgtgtaggcatgaaatgacttgtgattacccttttgatctatcctgaacaaggtttaagtaataaagtaatattattacacaataataagaacacactcacaaaacgaccgcaatggctatcgactcccattttgatttgtgcgcataacgg**

>prolog/011876660/0_10583
CTTCTAAGAGGGTCGAATTGCTGTCCAAAGTTAGAGTCAGATTTGTGTCCGAATTTTTACTGAAATTCT

5: so i think it is not a fasta file ,and i get erro:

[142041]$ DBdump -rh /public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/raw_reads.db >
[142041]$ DBdump -h /public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/raw_reads.db >
Traceback (most recent call last):
  File "/home/fanyucai/software/python/Python-v2.7.9/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/fanyucai/software/python/Python-v2.7.9/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/mains/report_pre_assembly.py", line 46, in <module>
    main()
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/mains/report_pre_assembly.py", line 40, in main
    do_report(**vars(ARGS))
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/mains/report_pre_assembly.py", line 16, in do_report
    report_dict = stats_preassembly.calc_dict(**kwds)
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/stats_preassembly.py", line 231, in calc_dict
    preads = read_lens_from_fofn(i_preads_fofn_fn)
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/stats_preassembly.py", line 104, in read_lens_from_fofn
    return list(sorted(itertools.chain.from_iterable(get_fasta_readlengths(fn) for fn in fns)))
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/stats_preassembly.py", line 104, in <genexpr>
    return list(sorted(itertools.chain.from_iterable(get_fasta_readlengths(fn) for fn in fns)))
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/stats_preassembly.py", line 35, in get_fasta_readlengths
    for record in f:
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/falcon_kit/FastaReader.py", line 162, in yield_fasta_records
    raise Exception("Invalid FASTA file {!r}".format(fn))
Exception: Invalid FASTA file '/public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/preads/cns_00001/cns_00001.fasta'
2017-10-27 12:41:07,497 - root - DEBUG - CD: '/public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/report' -> '/public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/report'
2017-10-27 12:41:07,498 - root - DEBUG - CD: '/public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/report' -> '/public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/report'
2017-10-27 12:41:07,499 - root - CRITICAL - Error in /home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/report/task.json',\n 'timeout': 60,\n 'tmpdir': None}"
Traceback (most recent call last):
  File "/home/fanyucai/software/python/Python-v2.7.9/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/fanyucai/software/python/Python-v2.7.9/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_task.py", line 166, in <module>
    main()
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_task.py", line 158, in main
    run(**vars(parsed_args))
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_task.py", line 112, in run
    run_cfg_in_tmpdir(cfg, tmpdir)
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_task.py", line 136, in run_cfg_in_tmpdir
    run_python_func(func, myinputs, myoutputs, parameters)
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_task.py", line 101, in run_python_func
    do_support.run_bash(script_fn)
  File "/home/fanyucai/software/falcon/lib/python2.7/site-packages/pypeflow/do_support.py", line 51, in run_bash
    raise Exception('{} <- {!r}'.format(rc, cmd))
Exception: 256 <- '/bin/bash -vex /public/land/Pacbio/yangshu/falcon_3000_3000/0-rawreads/report/run_report_pre_assembly.sh'