An ZeroDivisionError when I run fastqp.py

[EnzoAndree]

Dear, I just install fastqp and an error occurred when i run the script, this is the error.

fastqp Sanger_F_sample.fastq At 2186 bytes per read of 1086 length we estimate 96 reads in input file. Bin size (-s) set to 1. Traceback (most recent call last): File "/usr/local/bin/fastqp", line 11, in sys.exit(main()) File "/usr/local/lib/python2.7/site-packages/fastqp/cli.py", line 370, in main run(arguments) File "/usr/local/lib/python2.7/site-packages/fastqp/cli.py", line 270, in run cycle_nuc[i]['T']]) * 100 for i in positions] ZeroDivisionError: integer division or modulo by zero

Any idea why this error occurred? I use OSx, python 2.7.13 and a sample of the fastq file is on the attachment.

Regards Sanger_F.fastq.zip

[mdshw5]

Thanks for reporting this, and for sending the test data! I think I know what's going on here, but give me a day or two to push a new version with the fix.

[mdshw5]

I've just pushed a fix, and a new version (0.3) to PyPI. You should update using python install --upgrade fastqp and then give it another shot. Here's an example plot from the test data you sent:

[EnzoAndree]

WoW @mdshw5, it looks awesome. Nevertheless i can't get the full output of fastqp, I get this error.

Sanger_F.fastq NNNNN None 2748.42 /usr/local/lib/python2.7/site-packages/matplotlib/artist.py:879: MatplotlibDeprecationWarning: The set_axis_bgcolor function was deprecated in version 2.0. Use set_facecolor instead. return func(v) Traceback (most recent call last): File "/usr/local/bin/fastqp", line 11, in load_entry_point('fastqp==0.3.1', 'console_scripts', 'fastqp')() File "/usr/local/lib/python2.7/site-packages/fastqp/cli.py", line 409, in main run(arguments) File "/usr/local/lib/python2.7/site-packages/fastqp/cli.py", line 348, in run kmerplot(positions, cycle_kmers, zip_archive, [fields[0] for fields in bad_kmers], fig_kw) File "/usr/local/lib/python2.7/site-packages/fastqp/plots.py", line 493, in kmerplot 'axis_bgcolor': 'white'}, fig_kw) File "/usr/local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 1211, in subplots ax0 = fig.add_subplot(gs[0, 0], subplot_kw) File "/usr/local/lib/python2.7/site-packages/matplotlib/figure.py", line 1021, in add_subplot a = subplot_class_factory(projection_class)(self, *args, kwargs) File "/usr/local/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 73, in init self._axes_class.init(self, fig, self.figbox, kwargs) File "/usr/local/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 526, in init self.spines = self._gen_axes_spines() File "/usr/local/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 963, in _gen_axes_spines ('left', mspines.Spine.linear_spine(self, 'left')), File "/usr/local/lib/python2.7/site-packages/matplotlib/spines.py", line 469, in linear_spine result = cls(axes, spine_type, path, kwargs) File "/usr/local/lib/python2.7/site-packages/matplotlib/spines.py", line 54, in init super(Spine, self).init(kwargs) File "/usr/local/lib/python2.7/site-packages/matplotlib/patches.py", line 126, in init self.set_facecolor(facecolor) File "/usr/local/lib/python2.7/site-packages/matplotlib/patches.py", line 334, in set_facecolor self._set_facecolor(color) File "/usr/local/lib/python2.7/site-packages/matplotlib/patches.py", line 324, in _set_facecolor self._facecolor = colors.to_rgba(color, alpha) File "/usr/local/lib/python2.7/site-packages/matplotlib/colors.py", line 139, in to_rgba c = colors[int(c[1]) % len(colors)] ZeroDivisionError: integer division or modulo by zero

and ONLY this plots:

cycle_specific_base_composition.png cycle_specific_gc.png gc_distribution.png quality_score_distribution.png quality_score_heatmap.png quality_score_quantiles.png read_length_distribution.png

dear @mdshw5, this error appear only to me?

Regards

[kdoroschak]

@EnzoAndree @mdshw5 I am running across the same (more recent) issue, and can reproduce it on the above sample fastq file on fastqp (0.3.1).

[mdshw5]

I'll take a look and see if I can reproduce it. Can I ask what python version you're running?

[kdoroschak]

python 2.7.13 Anaconda 64-bit

[ghost]

@mdshw5 The problem is caused by an empty list if there are no "bad kmers". I have pushed a (hack-ish) solution #28 that will (temporarily) solve the problem until a better way is found.

[mdshw5]

Thanks @edawine for taking the time to look in to this. I'll merge your changes and push a new release! I do think an empty list is the correct solution, since I'm using a test of nonlinearity to define over-represented kmers.