expected output for example? #24
Description
I've installed the latest FAST-iCLIP and I'm still having a lot of problems. I'm just trying to run the example command on the example data:
$ fasticlip -i rawdata/example_MMhur_R1.fastq rawdata/example_MMhur_R2.fastq --GRCm38 -s docs/GRCm38/GRCm38_STAR/ -n MMhur -o results
I get:
- a "SettingWithCopyWarning" from pandas.
- bowtie gives me:
Performing Bowtie...
Result :
Error : 12466 reads; of these:
12466 (100.00%) were unpaired; of these:
12301 (98.68%) aligned 0 times
56 (0.45%) aligned exactly 1 time
109 (0.87%) aligned >1 times
1.32% overall alignment rate
Result :
Error : 100228 reads; of these:
100228 (100.00%) were unpaired; of these:
98946 (98.72%) aligned 0 times
381 (0.38%) aligned exactly 1 time
901 (0.90%) aligned >1 times
1.28% overall alignment rate
which looks very poor.
- a more sinister pandas error just after this:
Process mapped data
Traceback (most recent call last):
File "fasticlip/retroviralMapping.py", line 150, in <module>
bedR2=readBed(mappedBed[1])
File "fasticlip/retroviralMapping.py", line 143, in readBed
bedFile = pd.read_table(path,dtype=str,header=None)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 562, in parser_f
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 315, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 645, in __init__
self._make_engine(self.engine)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 799, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 1213, in __init__
self._reader = _parser.TextReader(src, **kwds)
File "pandas/parser.pyx", line 523, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:5214)
pandas.io.common.EmptyDataError: No columns to parse from file
Perhaps the pandas error is a consequence of the low alignment rate. What is the expected output? I get some output, but no figures are generated because of a matplotlib/Qt error (which I'll try to fix on my end before mentioning it here).