missing required option "save_path"

[turbo4xl]

when I run this command /mnt/c/Users/mdg.bio/Downloads/course_data/practicals/basecalling_practical$ guppy_basecaller –i ./fast5 –s ./guppy_out –c dna_r9.4.1_450bps_hac.cfg --num_callers 2 --cpu_threads_per_caller 1

error: missing required option "save_path" what I am doing wrong?

[timkahlke]

Hi turbo4xl,

The error message indicates that guppy doesn't recognise the -s options although it is part of the command you posted. Did you copy-paste the command? If so that is most likely the problem: the hyphen seems to be the wrong character/type. Please try the same command again but actually type the "-" for the -i and -s options. That should fix it.

[turbo4xl]

thanks much that fixed it. another problem occured with pycoQC fdelago@MDGFIRMINTEST2:/mnt/c/course_data/Practicals/qc_practical/summaries$ pycoQC -f summaries/run_1/sequence_summary.txt -o run_1.html

then had all there lines

Traceback (most recent call last): File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 574, in _build_master ws.require(requires) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 892, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 783, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (pysam 0.15.2 (/usr/local/lib/python3.6/dist-packages), Requirement.parse('pysam==0.15.3'), {'pycoQC'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/local/bin/pycoQC", line 6, in from pkg_resources import load_entry_point File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3088, in @_call_aside File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3072, in _call_aside f(*args, **kwargs) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3101, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 576, in _build_master return cls._build_from_requirements(requires) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 589, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 778, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'pysam==0.15.3' distribution was not found and is required by pycoQC

Any suggestion?

[turbo4xl]

issues with MinIonQC.R fdelago@MDGFIRMINTEST2:/mnt/c/course_data/Practicals/qc_practical$ MinIONQC.R –i qc_practical/summaries -o qc_practical/minion_qc

MinIONQC.R: command not found

[timkahlke]

Both errors indicate that PycoQC and MinIONQC are not properly installed. Did you set up the environment as described on the tutorial pages and use the Ubuntu install script I provided?

[turbo4xl]

Those previous errors stemmed from Ubuntu on WLS with the installation on the script. However I did an install using VM following all the steps that you indicated and ran into the same issues with PycoQC and MinIonQC. other commands seem to work so far. I have not finish the tuts all the way yet. I try to reinstall PycoQC and got a Exception traceback error from Python 2.7

[timkahlke]

PycoQC should be installed with Python3 not 2.7 (hence the pip3 in the install script). Anyway, I will check the installs in a fresh VM and come back to you then.

[turbo4xl]

running pip3 fdelago@MDGFIRMINTEST2:~$ pip3 install pycoQC Collecting pycoQC Downloading https://files.pythonhosted.org/packages/66/c4/5d9d579360da06cefd93f243a7f0187e4e85afe1fcf7990852737a6b818b/pycoQC-2.5.0.17.tar.gz Collecting h5py==2.9.0 (from pycoQC) Downloading https://files.pythonhosted.org/packages/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl (2.8MB) 100% |████████████████████████████████| 2.8MB 393kB/s Collecting jinja2==2.10.1 (from pycoQC) Downloading https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl (124kB) 100% |████████████████████████████████| 133kB 963kB/s Collecting numpy==1.17.1 (from pycoQC) Downloading https://files.pythonhosted.org/packages/75/92/57179ed45307ec6179e344231c47da7f3f3da9e2eee5c8ab506bd279ce4e/numpy-1.17.1-cp36-cp36m-manylinux1_x86_64.whl (20.4MB) 100% |████████████████████████████████| 20.4MB 103kB/s Collecting pandas==0.25.1 (from pycoQC) Downloading https://files.pythonhosted.org/packages/73/9b/52e228545d14f14bb2a1622e225f38463c8726645165e1cb7dde95bfe6d4/pandas-0.25.1-cp36-cp36m-manylinux1_x86_64.whl (10.5MB) 100% |████████████████████████████████| 10.5MB 189kB/s Collecting plotly==4.1.0 (from pycoQC) Downloading https://files.pythonhosted.org/packages/63/2b/4ca10995bfbdefd65c4238f9a2d3fde33705d18dd50914dd13302ec1daf1/plotly-4.1.0-py2.py3-none-any.whl (7.1MB) 100% |████████████████████████████████| 7.1MB 267kB/s Collecting pysam==0.15.3 (from pycoQC) Downloading https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz (3.2MB) 100% |████████████████████████████████| 3.2MB 518kB/s Collecting scipy==1.3.1 (from pycoQC) Downloading https://files.pythonhosted.org/packages/29/50/a552a5aff252ae915f522e44642bb49a7b7b31677f9580cfd11bcc869976/scipy-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (25.2MB) 100% |████████████████████████████████| 25.2MB 78kB/s Collecting tqdm==4.35.0 (from pycoQC) Downloading https://files.pythonhosted.org/packages/dc/88/d3213e2f3492daf09d8b41631ad6899f56db17ce83ea9c8a579902bafe5e/tqdm-4.35.0-py2.py3-none-any.whl (50kB) 100% |████████████████████████████████| 51kB 264kB/s Collecting six (from h5py==2.9.0->pycoQC) Using cached https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl Collecting MarkupSafe>=0.23 (from jinja2==2.10.1->pycoQC) Downloading https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl Collecting pytz>=2017.2 (from pandas==0.25.1->pycoQC) Using cached https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl Collecting python-dateutil>=2.6.1 (from pandas==0.25.1->pycoQC) Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl Collecting retrying>=1.3.3 (from plotly==4.1.0->pycoQC) Using cached https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz Building wheels for collected packages: pycoQC, pysam, retrying Running setup.py bdist_wheel for pycoQC ... done Stored in directory: /home/fdelago/.cache/pip/wheels/03/94/c6/90db083aef9e51abea2e6c40dfb87267f2739c2cbca37b590c Running setup.py bdist_wheel for pysam ... done Stored in directory: /home/fdelago/.cache/pip/wheels/85/ab/84/86ca6dda37a6fc85687b67be7345b735cd82f6584bea56f327 Running setup.py bdist_wheel for retrying ... done Stored in directory: /home/fdelago/.cache/pip/wheels/d7/a9/33/acc7b709e2a35caa7d4cae442f6fe6fbf2c43f80823d46460c Successfully built pycoQC pysam retrying Installing collected packages: six, numpy, h5py, MarkupSafe, jinja2, pytz, python-dateutil, pandas, retrying, plotly, pysam, scipy, tqdm, pycoQC Exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/usr/lib/python3/dist-packages/pip/commands/install.py", line 360, in run prefix=options.prefix_path, File "/usr/lib/python3/dist-packages/pip/req/req_set.py", line 784, in install **kwargs File "/usr/lib/python3/dist-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/usr/lib/python3/dist-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/usr/lib/python3/dist-packages/pip/wheel.py", line 247, in move_wheel_files prefix=prefix, File "/usr/lib/python3/dist-packages/pip/locations.py", line 153, in distutils_scheme i.finalize_options() File "/usr/share/python-wheels/setuptools-39.0.1-py2.py3-none-any.whl/setuptools/command/install.py", line 38, in finalize_options orig.install.finalize_options(self) File "/usr/lib/python3.6/distutils/command/install.py", line 351, in finalize_options self.create_home_path() File "/usr/lib/python3.6/distutils/command/install.py", line 581, in create_home_path os.makedirs(path, 0o700) File "/usr/lib/python3.6/os.py", line 210, in makedirs makedirs(head, mode, exist_ok) File "/usr/lib/python3.6/os.py", line 210, in makedirs makedirs(head, mode, exist_ok) File "/usr/lib/python3.6/os.py", line 220, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/home/fdelago/.local/lib'

[timkahlke]

I tested it and it seems the pycoQC problem is solved in the new install script. The solution for you is to run pip3 as you did but with "sudo"

sudo pip3 install pycoQC

That should fix it.

I can't reproduce your MinIONQC.R problem, that works fine everytime for me. Could you please check that you have the directory ~/github/minion_qc? If so please try to type ~/github/minion_qc/MinIONQC.R instead of just MinIONQC.R. That should do the trick.

[turbo4xl]

Thank you those two command work fine now in this line: pycoQC –f summaries/run_1/sequence_summary.txt –o run_1.html the files are named sequencing_summary.txt

[timkahlke]

Ha, nice, thanks :) will change that.

[peralesvilchezl]

hi, I have the same problem! when I run guppy 2021-09-16 17:54:37.928712 [guppy/info] crashpad_handler not supported on this platform. 2021-09-16 17:54:37.930003 [guppy/error] Unable to parse json: 2021-09-16 17:54:37.930045 [guppy/warning] An error has occurred. Aborting.