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FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.
GNU General Public License v3.0
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issue with references #30

Closed joergFLI closed 1 year ago

joergFLI commented 1 year ago

Hi, I am running into a problem with references.- freshly installed from conda today using conda install cansnper2=2.0.6 --channel bioconda --channel conda-forge --channel defaults --override-channels

and running

CanSNPer2 test.fasta --database CanSNPer2-data/database/francisella_tularensis.db

Run 1 alignments to references using progressiveMauve Traceback (most recent call last): File "/home/software/miniconda3/envs/cansnper2/lib/python3.11/site-packages/CanSNPer2/modules/CanSNPer2.py", line 346, in run xmfa_files = self.align(q) ^^^^^^^^^^^^^ File "/home/software/miniconda3/envs/cansnper2/lib/python3.11/site-packages/CanSNPer2/modules/CanSNPer2.py", line 192, in align commands,logs = self.create_mauve_command(query,references) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/software/miniconda3/envs/cansnper2/lib/python3.11/site-packages/CanSNPer2/modules/CanSNPer2.py", line 170, in create_mauve_command references = self.get_references() ^^^^^^^^^^^^^^^^^^^^^ File "/home/software/miniconda3/envs/cansnper2/lib/python3.11/site-packages/CanSNPer2/modules/CanSNPer2.py", line 100, in get_references return [ref for ref in os.listdir(self.refdir) if ref.endswith(".fna")] ^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'references/' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/software/miniconda3/envs/cansnper2/bin/CanSNPer2", line 10, in sys.exit(main()) ^^^^^^ File "/home/software/miniconda3/envs/cansnper2/lib/python3.11/site-packages/CanSNPer2/CanSNPerTree.py", line 164, in main CanSNPer2_obj.run(database=args.database) File "/home/software/miniconda3/envs/cansnper2/lib/python3.11/site-packages/CanSNPer2/modules/CanSNPer2.py", line 407, in run raise CanSNPer2Error("A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)") CanSNPer2.modules.CanSNPer2.CanSNPer2Error: 'A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next

Where should the folder "references" be located?

joergFLI commented 1 year ago

as additional information, please find my conda list below. Most packages are a bit more up-to-date compared to Carolines https://github.com/FOI-Bioinformatics/CanSNPer2/issues/19#issuecomment-633555359 but I do not see a major difference

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge ca-certificates 2020.4.5.1 hecc5488_0 conda-forge cansnper2 2.0.6 py_0 bioconda certifi 2020.4.5.1 py38h32f6830_0 conda-forge dbus 1.13.6 he372182_0 conda-forge ete3 3.1.1 py_1 conda-forge expat 2.2.9 he1b5a44_2 conda-forge flextaxd 0.2.1 py_0 bioconda fontconfig 2.13.1 h86ecdb6_1001 conda-forge freetype 2.10.1 he06d7ca_0 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge glib 2.64.2 h6f030ca_0 conda-forge gst-plugins-base 1.14.5 h0935bb2_2 conda-forge gstreamer 1.14.5 h36ae1b5_2 conda-forge icu 64.2 he1b5a44_1 conda-forge jpeg 9c h14c3975_1001 conda-forge ld_impl_linux-64 2.34 h53a641e_0 conda-forge libblas 3.8.0 16_openblas conda-forge libcblas 3.8.0 16_openblas conda-forge libclang 9.0.1 default_hde54327_0 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgfortran-ng 7.3.0 hdf63c60_5 conda-forge libiconv 1.15 h516909a_1006 conda-forge liblapack 3.8.0 16_openblas conda-forge libllvm9 9.0.1 he513fc3_1 conda-forge libopenblas 0.3.9 h5ec1e0e_0 conda-forge libpng 1.6.37 hed695b0_1 conda-forge libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxkbcommon 0.10.0 he1b5a44_0 conda-forge libxml2 2.9.10 hee79883_0 conda-forge libxslt 1.1.33 h31b3aaa_0 conda-forge llvm-openmp 10.0.0 hc9558a2_0 conda-forge lxml 4.5.0 py38hbb43d70_1 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge nspr 4.25 he1b5a44_0 conda-forge nss 3.47 he751ad9_0 conda-forge numpy 1.18.4 py38h8854b6b_0 conda-forge openssl 1.1.1g h516909a_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge pip 20.1 pyh9f0ad1d_0 conda-forge progressivemauve snapshot_2015_02_13 2 bioconda pthread-stubs 0.4 h14c3975_1001 conda-forge pyqt 5.12.3 py38ha8c2ead_2 conda-forge pyqt5-sip 4.19.18 pypi_0 pypi pyqtchart 5.12 pypi_0 pypi pyqtwebengine 5.12.1 pypi_0 pypi python 3.8.2 he5300dc_7_cpython conda-forge python_abi 3.8 1_cp38 conda-forge qt 5.12.5 hd8c4c69_1 conda-forge readline 8.0 hf8c457e_0 conda-forge scipy 1.4.1 py38h18bccfc_3 conda-forge setuptools 46.1.3 py38h32f6830_0 conda-forge six 1.14.0 py_1 conda-forge sqlite 3.30.1 hcee41ef_0 conda-forge tk 8.6.10 hed695b0_0 conda-forge wheel 0.34.2 py_1 conda-forge xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.9 h516909a_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.5 h516909a_0 conda-forge zlib 1.2.11 h516909a_1006 conda-forge

CarolineOhrman commented 1 year ago

Will try to see if I can understand whats wrong and come back to you!

CarolineOhrman commented 1 year ago

Hi Jörg! Have now tested but did not get these errors. I think you have missed the CanSNPer2-download command to get the folder with references (see below "CanSNPer2-download --database francisella_tularensis.db"). Before this command you can get a precompiled database from https://github.com/FOI-Bioinformatics/CanSNPer2-data (git clone repo) or make your own.

These are my commands and they seem to work. Could you test the same and see if you still have the same issue?

mamba create -n cansnper2 cansnper2
conda activate cansnper2
git clone https://github.com/FOI-Bioinformatics/CanSNPer2-data.git
cp CanSNPer2-data/database/francisella_tularensis.db .
CanSNPer2-download --database francisella_tularensis.db
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/886/065/GCF_002886065.1_ASM288606v1/GCF_002886065.1_ASM288606v1_genomic.fna.gz
gunzip GCF_002886065.1_ASM288606v1_genomic.fna.gz
CanSNPer2 --database francisella_tularensis.db GCF_002886065.1_ASM288606v1_genomic.fna

Output:

Run 1 alignments to references using progressiveMauve 2023-02-09 15:03:56,842 NewickTree [WARNI] #Node has no snp_annotation root GCF_002886065.1_ASM288606v1_genomic: B.51

CarolineOhrman commented 1 year ago

Resolved. The download will not download the database from the CanSNPer2-data git but only downloads the references defined in the references in the database (specified when creating the database in the references.txt file)