Hello, thanks for making this great software! I am using it for the first time, and I tried plotting my BlobDB.json file using this command:

blobtools plot -i /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.BlobDB.json -p 14 --out Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499

Here is the error message I received:

[STATUS] : Reading BlobDb /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.BlobDB.json [INFO] : no-hit : sequences = 156,883, span = 181.24 MB, N50 = 1,333 nt Traceback (most recent call last): File "/Users/cg449/Applications/blobtools/plot.py", line 183, in plotObj.plotBlobs(cov_lib, info_flag) File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 606, in plotBlobs plot_ref_legend(axScatter) File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 191, in plot_ref_legend axScatter.legend([ref_1,ref_2,ref3], ["1,000nt", "5,000nt", "10,000nt"], numpoints=1, loc = 4, fontsize=FONTSIZE) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/axes.py", line 4519, in legend self.legend = mlegend.Legend(self, handles, labels, kwargs) TypeError: init**() got an unexpected keyword argument 'fontsize'

Can you tell me what is wrong? I noticed that "fontsize=FONTSIZE" appeared many times in Btplot.py script, when maybe it should have been fontsize=35 or some other number. Thanks.

Hi,

Can you tell me what is wrong? I noticed that "fontsize=FONTSIZE" appeared many times in Btplot.py script, when maybe it should have been fontsize=35 or some other number. Thanks.

I am not sure what's wrong ... the "fontsize=FONTSIZE" bit should not be a problem since FONTSIZE gets declared at the top of BtPlot.py (and when I tested the last release it did not give a problem).

Could you

look whether "blobtools view" works on the BlobDb?
check that you have the latest release?

cheers, dom

Hi Dom,

Thanks for your quick reply. I deleted my existing blobtools folder and re-cloned blobtools from GitHub.

I re-ran the blobtools plot command and got the same error:

Output: [STATUS] : Reading BlobDb /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.BlobDB.json [INFO] : no-hit : sequences = 156,883, span = 181.24 MB, N50 = 1,333 nt Traceback (most recent call last): File "/Users/cg449/Applications/blobtools/plot.py", line 183, in plotObj.plotBlobs(cov_lib, info_flag) File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 608, in plotBlobs plot_ref_legend(axScatter) File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 190, in plot_ref_legend axScatter.legend([ref_1,ref_2,ref3], ["1,000nt", "5,000nt", "10,000nt"], numpoints=1, loc = 4, fontsize=FONTSIZE) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/axes.py", line 4519, in legend self.legend = mlegend.Legend(self, handles, labels, kwargs) TypeError: init**() got an unexpected keyword argument 'fontsize'

Blobtools view ran without error, but it gave me an output file with no phylum hits. I just realized that maybe it was because my "--taxfile" that I fed to blobtools create was in the blast output format that had "qseqids" and "staxids", but not the bitscore. Do you think that might be causing the error? I can re-do the BLAST run and try again. There is one thing I don't understand- why does the Blobtools paper recommend we use a random subset of contigs to save time during the BLAST run? How can all the contaminants be removed if they aren't all used as queries during the BLAST run?

Thanks so much, Christy

P.S. Blobtools view output:

##

assembly : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta

bam0 : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta.Tdactyloides2_no_rRNA.bowtie2.bam

tax0 : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/random10k.Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta.nt.1e-5.megablast

nodesDB : /Users/cg449/Applications/blobtools/data/nodesDB.txt

taxrule : bestsum

name length GC N bam0 phylum.t phylum.s phylum.c

TR12|c1_g1_i1 576 0.4028 0 0.996527777778 no-hit 0.0 None
TR14|c0_g1_i1 776 0.5399 0 13.3131443299 no-hit 0.0 None
TR39|c0_g1_i1 610 0.5066 0 64.0655737705 no-hit 0.0 None
TR58|c0_g1_i1 531 0.5499 0 4.66854990584 no-hit 0.0 None
TR82|c0_g1_i1 540 0.5407 0 2.6537037037 no-hit 0.0 None
TR91|c0_g1_i1 663 0.5822 0 5.69079939668 no-hit 0.0 None

Hi Dom,

I re-ran the blast against the nt database with my entire transcriptome dataset with the flag -outfmt '6 qseqid staxid bitscore'. I then ran blobtools create with the newest version of blobtools, and then blobtools plot. I still get that fontsize error:

Command:

blobtools plot -i /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides4_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.BlobDB.json -p 14 --out Tdactyloides4_no_roots_no_normalization_min_kmer_cov_2_greater_than_499

Output:

[STATUS] : Reading BlobDb /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides4_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.BlobDB.json [INFO] : Streptophyta : sequences = 124,919, span = 154.69 MB, N50 = 1,453 nt [INFO] : no-hit : sequences = 21,939, span = 17.96 MB, N50 = 807 nt [INFO] : Ascomycota : sequences = 4,143, span = 3.55 MB, N50 = 879 nt [INFO] : Chordata : sequences = 3,332, span = 2.91 MB, N50 = 896 nt [INFO] : Arthropoda : sequences = 2,311, span = 1.94 MB, N50 = 828 nt [INFO] : Eukaryota-undef : sequences = 32, span = 0.03 MB, N50 = 793 nt [INFO] : Nematoda : sequences = 23, span = 0.03 MB, N50 = 960 nt [INFO] : Actinobacteria : sequences = 16, span = 0.02 MB, N50 = 2,120 nt [INFO] : Platyhelminthes : sequences = 26, span = 0.02 MB, N50 = 744 nt [INFO] : Annelida : sequences = 26, span = 0.02 MB, N50 = 659 nt [INFO] : Proteobacteria : sequences = 22, span = 0.02 MB, N50 = 748 nt [INFO] : Bacteroidetes : sequences = 21, span = 0.01 MB, N50 = 716 nt [INFO] : Bacteria-undef : sequences = 13, span = 0.01 MB, N50 = 1,011 nt [INFO] : undef : sequences = 16, span = 0.01 MB, N50 = 659 nt [INFO] : other : sequences = 44, span = 0.03 MB, N50 = 723 nt Traceback (most recent call last): File "/Users/cg449/Applications/blobtools/plot.py", line 183, in plotObj.plotBlobs(cov_lib, info_flag) File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 608, in plotBlobs plot_ref_legend(axScatter) File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 190, in plot_ref_legend axScatter.legend([ref_1,ref_2,ref3], ["1,000nt", "5,000nt", "10,000nt"], numpoints=1, loc = 4, fontsize=FONTSIZE) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/axes.py", line 4519, in legend self.legend = mlegend.Legend(self, handles, labels, kwargs) TypeError: init**() got an unexpected keyword argument 'fontsize'

What do you recommend I do to get past this error?

Thanks, Christy

Hi Christy, sorry for not getting back earlier ...

Which version of matplotlib are you using?

could you run :

pip freeze | grep matplotlib

cheers,

dom

Hi,

That's OK thanks for helping!

I ran this command: pip freeze | grep matplotlib

Result:

/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/vendor/requests/packages/urllib3/util/ssl.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning matplotlib==1.1.1

Hi Christy,

this is most likely the problem, matplotlib 1.5 is required for running blobtools.

You could install "virtual env" in order to have a separate python environment so you can install matplotlib 1.5 and docopt independently for your main python installation

# install virtualenv 
pip install virtualenv

# clone blobtools into folder
git clone https://github.com/DRL/blobtools.git

# create virtual environment for blobtools  
cd blobtools/
virtualenv blob_env

# activate virtual environment
source blob_env/bin/activate

# install matplotlib
(blob_env) $ pip install matplotlib

# install docopt
(blob_env) $ pip install docopt 

# run
(blob_env) $ ./blobtools -h

Hello,

It still isn't working, even in the virtual environment. However, it is giving me a different error, which I suppose is progress. The error I get when I run blobtools plot is now: "UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128)". Below is my entire string of commands and their output, and blobtools plot is the last command. Any help would be greatly appreciated! Thanks.

Command: virtualenv blob_env3

Output: New python executable in blob_env3/bin/python Installing setuptools, pip, wheel...done.

Command: source blob_env3/bin/activate

Command (to try and solve the constant InsecurePlatformWarning I was getting): pip install --upgrade ndg-httpsclient

Output: Collecting ndg-httpsclient /Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning Collecting PyOpenSSL (from ndg-httpsclient) Using cached pyOpenSSL-0.15.1-py2.py3-none-any.whl Collecting six>=1.5.2 (from PyOpenSSL->ndg-httpsclient) Using cached six-1.10.0-py2.py3-none-any.whl Collecting cryptography>=0.7 (from PyOpenSSL->ndg-httpsclient) Using cached cryptography-1.2.1-cp27-none-macosx_10_6_intel.whl Collecting enum34 (from cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Collecting ipaddress (from cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Using cached ipaddress-1.0.16-py27-none-any.whl Collecting pyasn1>=0.1.8 (from cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Using cached pyasn1-0.1.9-py2.py3-none-any.whl Collecting setuptools>=1.0 (from cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Using cached setuptools-19.2-py2.py3-none-any.whl Collecting idna>=2.0 (from cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Using cached idna-2.0-py2.py3-none-any.whl Collecting cffi>=1.4.1 (from cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Using cached cffi-1.4.2-cp27-none-macosx_10_6_intel.whl Collecting pycparser (from cffi>=1.4.1->cryptography>=0.7->PyOpenSSL->ndg-httpsclient) Installing collected packages: six, enum34, ipaddress, pyasn1, setuptools, idna, pycparser, cffi, cryptography, PyOpenSSL, ndg-httpsclient Found existing installation: setuptools 18.2 Uninstalling setuptools-18.2: Successfully uninstalled setuptools-18.2 Successfully installed PyOpenSSL-0.15.1 cffi-1.4.2 cryptography-1.2.1 enum34-1.1.2 idna-2.0 ipaddress-1.0.16 ndg-httpsclient-0.4.0 pyasn1-0.1.9 pycparser-2.14 setuptools-19.2 six-1.10.0

Command (to try and solve the constant InsecurePlatformWarning I was getting): pip install pyopenssl ndg-httpsclient pyasn1

Output: Requirement already satisfied (use --upgrade to upgrade): pyopenssl in ./blob_env3/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): ndg-httpsclient in ./blob_env3/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): pyasn1 in ./blob_env3/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): six>=1.5.2 in ./blob_env3/lib/python2.7/site-packages (from pyopenssl) Requirement already satisfied (use --upgrade to upgrade): cryptography>=0.7 in ./blob_env3/lib/python2.7/site-packages (from pyopenssl) Requirement already satisfied (use --upgrade to upgrade): enum34 in ./blob_env3/lib/python2.7/site-packages (from cryptography>=0.7->pyopenssl) Requirement already satisfied (use --upgrade to upgrade): ipaddress in ./blob_env3/lib/python2.7/site-packages (from cryptography>=0.7->pyopenssl) Requirement already satisfied (use --upgrade to upgrade): setuptools>=1.0 in ./blob_env3/lib/python2.7/site-packages (from cryptography>=0.7->pyopenssl) Requirement already satisfied (use --upgrade to upgrade): idna>=2.0 in ./blob_env3/lib/python2.7/site-packages (from cryptography>=0.7->pyopenssl) Requirement already satisfied (use --upgrade to upgrade): cffi>=1.4.1 in ./blob_env3/lib/python2.7/site-packages (from cryptography>=0.7->pyopenssl) Requirement already satisfied (use --upgrade to upgrade): pycparser in ./blob_env3/lib/python2.7/site-packages (from cffi>=1.4.1->cryptography>=0.7->pyopenssl) (blob_env3)rs-btcg449lt:blobtools cg449$ pip install matplotlib Collecting matplotlib Using cached matplotlib-1.5.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting numpy>=1.6 (from matplotlib) Using cached numpy-1.10.4-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting pytz (from matplotlib) Using cached pytz-2015.7-py2.py3-none-any.whl Collecting python-dateutil (from matplotlib) Using cached python_dateutil-2.4.2-py2.py3-none-any.whl Collecting cycler (from matplotlib) Using cached cycler-0.9.0-py2.py3-none-any.whl Collecting pyparsing!=2.0.0,!=2.0.4,>=1.5.6 (from matplotlib) Using cached pyparsing-2.0.7-py2.py3-none-any.whl Requirement already satisfied (use --upgrade to upgrade): six>=1.5 in ./blob_env3/lib/python2.7/site-packages (from python-dateutil->matplotlib) Installing collected packages: numpy, pytz, python-dateutil, cycler, pyparsing, matplotlib Successfully installed cycler-0.9.0 matplotlib-1.5.1 numpy-1.10.4 pyparsing-2.0.7 python-dateutil-2.4.2 pytz-2015.7

Command: pip install docopt

Output: Collecting docopt Installing collected packages: docopt Successfully installed docopt-0.6.2

Command: blobtools plot -i /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499_virtualenv.BlobDB.json -p 14 --out Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499_virtualenv /Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') Traceback (most recent call last): File "/Users/cg449/Applications/blobtools/plot.py", line 57, in import lib.BtPlot as BtPlot File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 22, in import matplotlib.pyplot as plt File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/pyplot.py", line 29, in import matplotlib.colorbar File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/colorbar.py", line 34, in import matplotlib.collections as collections File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/collections.py", line 27, in import matplotlib.backend_bases as backend_bases File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 62, in import matplotlib.textpath as textpath File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/textpath.py", line 15, in import matplotlib.font_manager as font_manager File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1421, in _rebuild() File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1406, in _rebuild fontManager = FontManager() File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1044, in init self.ttffiles = findSystemFonts(paths) + findSystemFonts() File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/font_manager.py", line 324, in findSystemFonts for f in get_fontconfig_fonts(fontext): File "/Users/cg449/Applications/blobtools/blob_env3/lib/python2.7/site-packages/matplotlib/font_manager.py", line 276, in get_fontconfig_fonts stderr=subprocess.PIPE) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128)

Hi Christy,

could it be that the error messages are incomplete (e.g there is a closing bracket in the fifth line from the bottom that does not have an opening bracket). It is very hard to figure out what's going on without having all information.

Can you sent me the last part again? Also, what OS version are you using? Have you checked that matplotlib 1.5.1 is now installed correctly (using pip freeze)?

cheers,

dom

Hello,

I'm not sure why that closing bracket is missing. It looks that way in my terminal as well. I ran everything again and I'm just going to copy and paste my entire terminal here so you can see it. As it says below, I am running matplotlib 1.5.1 in the virtual environment. I am using OS X 10.9.5.

Here is all the text from my terminal, unedited:

rs-btcg449lt:blobtools cg449$ virtualenv blob_env4 New python executable in blob_env4/bin/python Installing setuptools, pip, wheel...done. rs-btcg449lt:blobtools cg449$ source blob_env4/bin/activate (blob_env4)rs-btcg449lt:blobtools cg449$ pip install matplotlib Collecting matplotlib /Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning Using cached matplotlib-1.5.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting numpy>=1.6 (from matplotlib) Using cached numpy-1.10.4-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting pytz (from matplotlib) Using cached pytz-2015.7-py2.py3-none-any.whl Collecting python-dateutil (from matplotlib) Using cached python_dateutil-2.4.2-py2.py3-none-any.whl Collecting cycler (from matplotlib) Using cached cycler-0.9.0-py2.py3-none-any.whl Collecting pyparsing!=2.0.0,!=2.0.4,>=1.5.6 (from matplotlib) Using cached pyparsing-2.0.7-py2.py3-none-any.whl Collecting six>=1.5 (from python-dateutil->matplotlib) Using cached six-1.10.0-py2.py3-none-any.whl Installing collected packages: numpy, pytz, six, python-dateutil, cycler, pyparsing, matplotlib Successfully installed cycler-0.9.0 matplotlib-1.5.1 numpy-1.10.4 pyparsing-2.0.7 python-dateutil-2.4.2 pytz-2015.7 six-1.10.0 /Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning (blob_env4)rs-btcg449lt:blobtools cg449$ pip freeze | grep matplotlib matplotlib==1.5.1 (blob_env4)rs-btcg449lt:blobtools cg449$ pip install docopt Collecting docopt /Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning Installing collected packages: docopt Successfully installed docopt-0.6.2 (blob_env4)rs-btcg449lt:blobtools cg449$ ./blobtools plot -i /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499_virtualenv.BlobDB.json -p 14 --out Trinity_assembly_no_root_libraries/Tdactyloides2_no_roots_no_normalization_min_kmer_cov_2_greater_than_499_virtualenv_blobplot /Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') Traceback (most recent call last): File "./plot.py", line 57, in import lib.BtPlot as BtPlot File "/Users/cg449/Applications/blobtools/lib/BtPlot.py", line 22, in import matplotlib.pyplot as plt File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/pyplot.py", line 29, in import matplotlib.colorbar File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/colorbar.py", line 34, in import matplotlib.collections as collections File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/collections.py", line 27, in import matplotlib.backend_bases as backend_bases File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 62, in import matplotlib.textpath as textpath File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/textpath.py", line 15, in import matplotlib.font_manager as font_manager File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1421, in _rebuild() File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1406, in _rebuild fontManager = FontManager() File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1044, in init self.ttffiles = findSystemFonts(paths) + findSystemFonts() File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/font_manager.py", line 324, in findSystemFonts for f in get_fontconfig_fonts(fontext): File "/Users/cg449/Applications/blobtools/blob_env4/lib/python2.7/site-packages/matplotlib/font_manager.py", line 276, in get_fontconfig_fonts stderr=subprocess.PIPE) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) (blob_env4)rs-btcg449lt:blobtools cg449$

I noticed that the bold "init" in the error message is surrounded by two underscores on either side in my terminal, but it isn't showing up right when I paste it. For some reason, the github website is converting the text that looks like "underscore underscore init underscore underscore" into simply a bold init. I only noticed because it was in the line of the error message you were referring to that looked incomplete. Actually, now that I look closer, a lot of text in the error message is getting converted to special fonts like italics when I past them into the website.

I attached a text document of the error, to get around this communication problem:

blobology_error.txt

Hi there, I am also encountering an error with the Font building matplotlib (It is the newer 1.5.1 version which I have installed). Error reads as follows:

Traceback (most recent call last): File "./plot.py", line 57, in import lib.BtPlot as BtPlot File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/lib/BtPlot.py", line 22, in import matplotlib.pyplot as plt File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/pyplot.py", line 29, in import matplotlib.colorbar File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/colorbar.py", line 34, in import matplotlib.collections as collections File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/collections.py", line 27, in import matplotlib.backend_bases as backend_bases File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 62, in import matplotlib.textpath as textpath File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/textpath.py", line 15, in import matplotlib.font_manager as font_manager File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1421, in _rebuild() File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1408, in _rebuild pickle_dump(fontManager, _fmcache) File "/mnt/ris-fas1a/linux_groups2/freeman_grp/Blobs/blobtools/blob_env/lib/python2.7/site-packages/matplotlib/font_manager.py", line 957, in pickle_dump pickle.dump(data, fh) IOError: [Errno 122] Disk quota exceeded

In the case that this is also coming up as special text, attached is a text file of the error. Blobs Error.txt

Hi,

these errors are due to problems with the matplotlib installation.

cheers,

dom

DRL / blobtools

blobtools plot: init() got an unexpected keyword argument 'fontsize' #8

assembly : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta

bam0 : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta.Tdactyloides2_no_rRNA.bowtie2.bam

tax0 : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/random10k.Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta.nt.1e-5.megablast

nodesDB : /Users/cg449/Applications/blobtools/data/nodesDB.txt

taxrule : bestsum

name length GC N bam0 phylum.t phylum.s phylum.c

DRL / blobtools

blobtools plot: __init__() got an unexpected keyword argument 'fontsize' #8

assembly : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta

bam0 : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta.Tdactyloides2_no_rRNA.bowtie2.bam

tax0 : /Users/cg449/Desktop/Tripsacum/transcriptome_assembly/Tdactyloides/Trinity_assembly_no_root_libraries/random10k.Trinity_Tdactyloides_no_roots_no_normalization_min_kmer_cov_2_greater_than_499.fasta.nt.1e-5.megablast

nodesDB : /Users/cg449/Applications/blobtools/data/nodesDB.txt

taxrule : bestsum

name length GC N bam0 phylum.t phylum.s phylum.c

blobtools plot: init() got an unexpected keyword argument 'fontsize' #8