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Retrieving gene annotation for hg38
Expecting 10 words line 1 of /dev/stdin got 9
cut: write error: Broken pipe
Downloading hg38 genome
Trying to download http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/chromFa.tar.gz
Trying to download http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
´Unpacking
Creating index
Sorry, can only index genomes with one sequence per FASTA file
/cbscratch/croth1/gimmemotifs/genomes/hg38/hg38/hg38.fa contains multiple sequences

======================================================================

ERROR: test1_denovo (test_denovo.TestDenovo)

de novo motif prediction

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/travis/build/simonvh/gimmemotifs/test/test_denovo.py", line 28, in test1_denovo

    cluster=True)

  File "/home/travis/build/simonvh/gimmemotifs/gimmemotifs/denovo.py", line 559, in gimme_motifs

    stats,

  File "/home/travis/build/simonvh/gimmemotifs/gimmemotifs/report.py", line 219, in create_denovo_motif_report

    _create_text_report(inputfile, motifs, closest_match, stats, outdir)

  File "/home/travis/build/simonvh/gimmemotifs/gimmemotifs/report.py", line 87, in _create_text_report

    my_stats[str(motif)][bg] = stats[str(motif)][bg].copy()

KeyError: 'GimmeMotifs_6_ACTyAAACCG'

reading mapping
Traceback (most recent call last):
  File "/home/carlos/anaconda2/envs/gimme/bin/gimme", line 496, in <module>
    args.func(args)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/commands/roc.py", line 143, in roc
    0.01,
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/commands/roc.py", line 71, in html_report
    f.write(df.sort_values("ROC AUC", ascending=False).style.bar(bar_cols).set_precision(3).set_table_attributes("data-sortable").render().replace("data-sortable", 'class="sortable-theme-slick" data-sortable'))
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/pandas/io/formats/style.py", line 434, in render
    self._compute()
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/pandas/io/formats/style.py", line 502, in _compute
    r = func(self)(*args, **kwargs)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/pandas/io/formats/style.py", line 531, in _apply
    raise ValueError(msg)
ValueError: Function <function Styler._bar_left at 0x7f4cdc455ae8> returned the wrong shape.
Result has shape: (6,)
Expected shape:   (0, 6)

galaxy_env)solexa@gecko:/groups/csf-ngs/bin/gimmemotifs/gimmemotifs-0.8.4/src/MoAn$ make
gcc -c -g -W  -O3 anneal.c -o obj/anneal.o
gcc -c -g -W  -O3 sesa.c -o obj/sesa.o
gcc -c -g -W  -O3 score.c -o obj/score.o
gcc -c -g -W  -O3 build.c -o obj/build.o
gcc -c -g -W  -O3 search.c -o obj/search.o
gcc -c -g -W  -O3 hittable.c -o obj/hittable.o
gcc -c -g -W  -O3 pssm.c -o obj/pssm.o
gcc -c -g -W  -O3 timer.c -o obj/timer.o
gcc -c -g -W  -O3 error.c -o obj/error.o
gcc -c -g -W  -O3 stringcon.c -o obj/stringcon.o
gcc -c -g -W  -O3 ds_ssort/globals.c -o obj/globals.o
gcc -c -g -W  -O3 ds_ssort/ds.c -o obj/ds.o
gcc -c -g -W  -O3 ds_ssort/shallow.c -o obj/shallow.o
ds_ssort/shallow.c: In function ‘shallow_mkq’:
ds_ssort/shallow.c:92:19: error: nested function ‘vecswap2’ declared but never defined
ds_ssort/shallow.c: In function ‘shallow_mkq16’:
ds_ssort/shallow.c:186:19: error: nested function ‘vecswap2’ declared but never defined
ds_ssort/shallow.c: In function ‘shallow_mkq32’:
ds_ssort/shallow.c:264:19: error: nested function ‘vecswap2’ declared but never defined
ds_ssort/shallow.c: In function ‘shallow_inssort_lcp’:
ds_ssort/shallow.c:498:20: error: nested function ‘cmp_unrolled_shallow_lcp’ declared but never defined
make: *** [obj/shallow.o] Error 1

(galaxy_env)solexa@gecko:/groups/csf-ngs/bin/gimmemotifs/gimmemotifs-0.8.4/src/MoAn$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.7/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.7.2-5' --with-bugurl=file:///usr/share/doc/gcc-4.7/README.Bugs --enable-languages=c,c++,go,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.7 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.7 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --with-arch-32=i586 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.7.2 (Debian 4.7.2-5)

cd /home/george
virtualenv GimmeMotifs_pythonEnv
GimmeMotifs_pythonEnv/bin/pip install numpy # 1.11.0
GimmeMotifs_pythonEnv/bin/pip install scipy # 0.17.1
GimmeMotifs_pythonEnv/bin/pip install matplotlib # 1.5.1
GimmeMotifs_pythonEnv/bin/pip install kid # 0.9.6
GimmeMotifs_pythonEnv/bin/pip install pybedtools # 0.7.7
GimmeMotifs_pythonEnv/bin/pip install pandas # 0.18.1
GimmeMotifs_pythonEnv/bin/pip install gimmemotifs # 0.9.0.3

source /home/george/GimmeMotifs_pythonEnv/bin/activate

gimme motifs /home/george/GimmeMotifs_pythonEnv/share/gimmemotifs/examples/TAp73alpha.fa -n /home/george/gimmemotifs_test/p73

Traceback (most recent call last):
  File "/home/george/GimmeMotifs_pythonEnv/bin/gimme", line 11, in <module>
    from  gimmemotifs import commands
  File "/home/george/GimmeMotifs_pythonEnv/local/lib/python2.7/site-packages/gimmemotifs/commands/__init__.py", line 8, in <module>
    m =  __import__("{0}.{1}".format(__name__, cmdname), globals(), locals(), [cmdname], -1)
  File "/home/george/GimmeMotifs_pythonEnv/local/lib/python2.7/site-packages/gimmemotifs/commands/cluster.py", line 11, in <module>
    from gimmemotifs.comparison import MotifComparer
  File "/home/george/GimmeMotifs_pythonEnv/local/lib/python2.7/site-packages/gimmemotifs/comparison.py", line 419, in <module>
    from gimmemotifs.mp import pool
  File "/home/george/GimmeMotifs_pythonEnv/local/lib/python2.7/site-packages/gimmemotifs/mp.py", line 5, in <module>
    n_cpus = int(MotifConfig().get_default_params()["ncpus"])
KeyError: 'ncpus'

>>> MotifConfig().get_default_params()
{'fraction': '0.2', 'use_strand': 'False', 'available_tools': 'MDmodule,MEME,GADEM,MotifSampler,trawler,Improbizer,BioProspector,Posmo,ChIPMunk,JASPAR,AMD,HMS,Homer', 'abs_max': '1000', 'analysis': 'medium', 'pvalue': '0.001', 'width': '200', 'lwidth': '500', 'scan_cutoff': '0.9', 'background': 'genomic_matched,random', 'cluster_threshold': '0.95', 'max_time': 'None', 'motif_db': 'vertebrate_motifs.pwm', 'tools': 'MDmodule,MEME,MotifSampler,trawler,Improbizer,BioProspector,Posmo,ChIPMunk,JASPAR,AMD,HMS,Homer', 'enrichment': '1.5', 'markov_model': '1', 'genome': 'hg19'}

Retrieving gene annotation for hg18
Using http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz
zcat /tmp/tmpKPJNfT.gz | cut -f1-11 | /home/carlos/anaconda2/bin/genePredToBed /dev/stdin /home/carlos/anaconda2/share/gimmemotifs/genes/hg18.bed
Downloading hg18 genome
Trying to download http://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/chromFa.tar.gz
Trying to download http://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/hg18.fa.gz
Failed to download genome

/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/matplotlib/font_manager.py:280: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  'Matplotlib is building the font cache using fc-list. '
Retrieving gene annotation for hg18
Using http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz
zcat /tmp/tmpn1pj049r.gz | cut -f1-11 | /home/carlos/anaconda2/envs/gimme/bin/genePredToBed /dev/stdin /home/carlos/anaconda2/envs/gimme/share/gimmemotifs/genes/hg18.bed
Downloading hg18 genome
Trying to download http://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/chromFa.tar.gz
Traceback (most recent call last):
  File "/home/carlos/anaconda2/envs/gimme/bin/gimme", line 496, in <module>
    args.func(args)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/commands/genome.py", line 23, in genome
    get_genome(args.genomebuild, args.fastadir, args.indexdir)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/genome_index.py", line 222, in get_genome
    download_genome(genomebuild, genome_dir)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/genome_index.py", line 168, in download_genome
    genome_fa
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 248, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 532, in open
    response = meth(req, response)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 642, in http_response
    'http', request, response, code, msg, hdrs)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 570, in error
    return self._call_chain(*args)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/home/carlos/anaconda2/envs/gimme/lib/python3.6/urllib/request.py", line 650, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found

def create_background(self, background=["random"], organism="hg18", width=200):
    nr_sequences = {}

# Create background for motif prediction
if "gc" in background:
     #this is the line I am talking about; self.validation_fa should be self.prediction_fa
    self._create_background("gc", self.validation_bed, self.validation_fa, self.prediction_bg,  organism=organism, width=width)

else:
    #this is the line I am talking about; self.validation_fa should be self.prediction_fa
    self._create_background(background[0], self.validation_bed, self.validation_fa, self.prediction_bg, organism=organism, width=width)

# Get background fasta files
for bg in background:
    nr_sequences[bg] = self._create_background(bg, self.validation_bed, self.validation_fa, self.bg_file["fa"][bg], organism=organism, width=width)