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DessimozLab / fold_tree

snakemake pipeline for creating trees from sequence sets
MIT License
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AttributeError: 'function' object has no attribute 'palette'. Did you mean: 'palettes'? #10

Closed BinhongLiu closed 11 months ago

BinhongLiu commented 11 months ago

Hi, I've prepared the environment based on the fold_tree.yaml and the installed packages are here:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohttp 3.9.1 py310h2372a71_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge amply 0.1.6 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argtable2 2.13 h14c3975_1001 conda-forge aria2 1.37.0 h347180d_1 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge bcrypt 4.1.1 py310hcb5633a_0 conda-forge biopython 1.81 py310h2372a71_1 conda-forge black 23.11.0 py310hff52083_0 conda-forge boto3 1.33.11 pyhd8ed1ab_0 conda-forge botocore 1.33.11 pyhd8ed1ab_0 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.23.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge cachetools 5.3.2 pyhd8ed1ab_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge clustalo 1.2.4 hdbdd923_7 bioconda coin-or-cbc 2.10.10 h9002f0b_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.8 ha2443b9_0 conda-forge coin-or-utils 2.11.9 hee58242_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge colormath 3.0.0 pypi_0 pypi configargparse 1.7 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 41.0.7 py310hb8475ec_1 conda-forge datrie 0.8.2 py310h2372a71_7 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge deprecated 1.2.14 pyh1a96a4e_0 conda-forge docutils 0.20.1 py310hff52083_3 conda-forge dpath 2.1.6 pyha770c72_0 conda-forge dropbox 11.36.2 pyhd8ed1ab_0 conda-forge eido 0.2.2 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fasttree 2.1.11 h031d066_2 bioconda filechunkio 1.8 py_2 conda-forge foldseek 8.ef4e960 pl5321hb365157_0 bioconda font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_1 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 h267a509_2 conda-forge frozenlist 1.4.0 py310h2372a71_1 conda-forge ftputil 5.0.4 pyhd8ed1ab_0 conda-forge future 0.18.3 pypi_0 pypi gawk 5.3.0 ha916aea_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gitdb 4.0.11 pyhd8ed1ab_0 conda-forge gitpython 3.1.40 pyhd8ed1ab_0 conda-forge gmp 6.3.0 h59595ed_0 conda-forge google-api-core 2.15.0 pyhd8ed1ab_0 conda-forge google-api-python-client 2.110.0 pyhd8ed1ab_0 conda-forge google-auth 2.25.2 pyhca7485f_0 conda-forge google-auth-httplib2 0.1.1 pyhd8ed1ab_0 conda-forge google-cloud-core 2.4.1 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.13.0 pyhca7485f_0 conda-forge google-crc32c 1.1.2 py310hc5c09a0_5 conda-forge google-resumable-media 2.6.0 pyhd8ed1ab_0 conda-forge googleapis-common-protos 1.62.0 pyhd8ed1ab_0 conda-forge grpcio 1.60.0 py310h1b8f574_0 conda-forge httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 pyhd8ed1ab_6 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.6 pyhd8ed1ab_0 conda-forge importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge iqtree 2.2.6 h21ec9f0_0 bioconda jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.5.0 py310hff52083_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libabseil 20230802.1 cxx17_h59595ed_0 conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libglib 2.78.3 h783c2da_0 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libgrpc 1.60.0 hd6c4280_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge liblapacke 3.9.0 20_linux64_openblas conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 4.24.4 hf27288f_0 conda-forge libre2-11 2023.06.02 h7a70373_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxml2 2.12.2 h232c23b_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py310h2372a71_1 conda-forge mdurl 0.1.0 pyhd8ed1ab_0 conda-forge mpfr 4.2.1 h9458935_0 conda-forge multidict 6.0.4 py310h2372a71_1 conda-forge muscle 5.1 h4ac6f70_3 bioconda mypy_extensions 1.0.0 pyha770c72_0 conda-forge nbformat 5.9.2 pyhd8ed1ab_0 conda-forge ncurses 6.4 h59595ed_2 conda-forge networkx 3.2.1 pypi_0 pypi numpy 1.26.2 py310hb13e2d6_0 conda-forge oauth2client 4.1.3 py_0 conda-forge openssl 3.2.0 hd590300_1 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.1.4 py310hcc13569_0 conda-forge paramiko 3.3.1 pyhd8ed1ab_0 conda-forge pathspec 0.12.1 pyhd8ed1ab_0 conda-forge patsy 0.5.4 pypi_0 pypi pcre2 10.42 hcad00b1_0 conda-forge peppy 0.35.7 pyhd8ed1ab_0 conda-forge perl 5.32.1 4_hd590300_perl5 conda-forge pip 23.3.1 pyhd8ed1ab_0 conda-forge pixman 0.42.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge plac 1.4.2 pyhd8ed1ab_0 conda-forge platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge ply 3.11 py_1 conda-forge prettytable 3.9.0 pyhd8ed1ab_0 conda-forge protobuf 4.24.4 py310h620c231_0 conda-forge psutil 5.9.5 py310h2372a71_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulp 2.7.0 py310hff52083_1 conda-forge pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge pycairo 1.25.1 py310hda9f760_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygithub 2.1.1 pyhd8ed1ab_0 conda-forge pygments 2.17.2 pyhd8ed1ab_0 conda-forge pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge pynacl 1.5.0 py310h2372a71_3 conda-forge pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.4.3 pyhd8ed1ab_0 conda-forge python 3.10.13 hd12c33a_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge python-irodsclient 1.1.9 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge quicktree 2.5 h031d066_4 bioconda re2 2023.06.02 h2873b5e_0 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.32.0 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge reretry 0.11.8 pyhd8ed1ab_0 conda-forge rich 13.7.0 pyhd8ed1ab_0 conda-forge rpds-py 0.13.2 py310hcb5633a_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge s3transfer 0.8.2 pyhd8ed1ab_0 conda-forge scipy 1.11.4 py310hb13e2d6_0 conda-forge setuptools 68.2.2 pyhd8ed1ab_0 conda-forge setuptools-scm 8.0.4 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge slacker 0.14.0 py_0 conda-forge smart_open 6.4.0 pyhd8ed1ab_0 conda-forge smmap 5.0.0 pyhd8ed1ab_0 conda-forge snakedeploy 0.9.1 pyhdfd78af_0 bioconda snakefmt 0.8.5 pyhdfd78af_0 bioconda snakemake 7.32.4 hdfd78af_1 bioconda snakemake-minimal 7.32.4 pyhdfd78af_1 bioconda statsmodels 0.14.0 pypi_0 pypi stone 3.3.1 pyhd8ed1ab_0 conda-forge stopit 1.1.2 py_0 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge throttler 1.2.2 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toposort 1.10 pyhd8ed1ab_0 conda-forge toyplot 0.2.0 pypi_0 pypi toytree 2.0.1 pypi_0 pypi tqdm 4.66.1 pypi_0 pypi traitlets 5.14.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.9.0 hd8ed1ab_0 conda-forge typing_extensions 4.9.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ubiquerg 0.6.3 pyhd8ed1ab_0 conda-forge uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge urllib3 1.26.18 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge wget 3.2 pypi_0 pypi wheel 0.42.0 pyhd8ed1ab_0 conda-forge wrapt 1.16.0 py310h2372a71_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.9.3 py310h2372a71_0 conda-forge yte 1.5.4 pyha770c72_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge

However, I encountered an error when testing with the four AF2 models: A0A060X1A3 A0A087X979 A0A091CQV1 A0A091F6W6

the log is here: (foldtree) [ac1daawz21@login05 fold_tree]$ snakemake --cores 4 --use-conda -s ./workflow/fold_tree --config folder=./myfam filter=False foldseek_cores=4 /work/home/ac1daawz21/software/fold_tree/ Config file /work/home/ac1daawz21/software/fold_tree/workflow/config/config_vars.yaml is extended by additional config specified via the command line. Building DAG of jobs... Relative file path './myfam/plddt.json' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/finalset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/plddt.json' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/plddt.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/sequence_dataset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/sequences.fst' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/finalset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/dlstructs.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/identifiers.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/sequence_dataset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/dlsequences.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldtree_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldtree_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldtree_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/allvall_1.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/foldtree_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldseek2distmat.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/finalset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/allvall_1.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldseekallvall.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/alntmscore_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/alntmscore_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/alntmscore_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/alntmscore_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/lddt_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/lddt_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/lddt_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/lddt_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/plddt.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/dlstructs.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/dlsequences.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldtree_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldtree_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldtree_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldseek2distmat.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/foldseekallvall.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/alntmscore_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/alntmscore_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/alntmscore_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/lddt_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/lddt_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Relative file path './myfam/logs/lddt_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths. Using shell: /usr/bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Job stats: job count

all 1 dl_ids_sequences 1 dl_ids_structs 1 foldseek2distmat 1 foldseek_allvall_1 1 mad_root_post 3 plddt 1 postprocess 3 quicktree 3 total 15

Select jobs to execute...

[Mon Dec 11 22:30:53 2023] rule dl_ids_sequences: input: ./myfam/identifiers.txt output: ./myfam/sequence_dataset.csv log: ./myfam/logs/dlsequences.log jobid: 3 reason: Missing output files: ./myfam/sequence_dataset.csv wildcards: folder=./myfam resources: tmpdir=/tmp

/work/home/ac1daawz21/miniconda3/lib/python3.8/site-packages/requests/init.py:102: RequestsDependencyWarning: urllib3 (1.26.8) or chardet (5.2.0)/charset_normalizer (2.0.4) doesn't match a supported version! warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported " Activating conda environment: foldtree Activating conda environment: foldtree custom_structs: False Entry Name Entry ... Sequence query 0 A0A091CQV1_FUKDA A0A091CQV1 ... MYELSIVAVPTDGNAGLLAEPQIAMFCGKLNMHMNVQNGKWEPDPS... A0A091CQV1 1 A0A060X1A3_ONCMY A0A060X1A3 ... MGDRMALLLLVVATSALAVEVPTDGGMGLLAEPQVAMFCGKLNMHV... A0A060X1A3 2 A0A087X979_POEFO A0A087X979 ... LRAETKFYLLGQVCQALVMRVPADVSMGLLAEPQVAMFCGKLNMHI... A0A087X979 3 A0A091F6W6_CORBR A0A091F6W6 ... SFQVPADGNAGLLAEPQIAMFCGKLNMHMNVQNGKWESDPSGTKTC... A0A091F6W6

[4 rows x 10 columns] Entry Name Entry ... Sequence query 0 A0A091CQV1_FUKDA A0A091CQV1 ... MYELSIVAVPTDGNAGLLAEPQIAMFCGKLNMHMNVQNGKWEPDPS... A0A091CQV1 1 A0A060X1A3_ONCMY A0A060X1A3 ... MGDRMALLLLVVATSALAVEVPTDGGMGLLAEPQVAMFCGKLNMHV... A0A060X1A3 2 A0A087X979_POEFO A0A087X979 ... LRAETKFYLLGQVCQALVMRVPADVSMGLLAEPQVAMFCGKLNMHI... A0A087X979 3 A0A091F6W6_CORBR A0A091F6W6 ... SFQVPADGNAGLLAEPQIAMFCGKLNMHMNVQNGKWESDPSGTKTC... A0A091F6W6

[4 rows x 10 columns] [Mon Dec 11 22:31:46 2023] Finished job 3. 1 of 15 steps (7%) done Select jobs to execute...

[Mon Dec 11 22:31:46 2023] rule dl_ids_structs: input: ./myfam/sequence_dataset.csv output: ./myfam/sequences.fst, ./myfam/finalset.csv log: ./myfam/logs/dlstructs.log jobid: 2 reason: Missing output files: ./myfam/finalset.csv; Input files updated by another job: ./myfam/sequence_dataset.csv wildcards: folder=./myfam resources: tmpdir=/tmp

Activating conda environment: foldtree Activating conda environment: foldtree -1 / unknownmissing in afdb: set() missing in sequences: set() [Mon Dec 11 22:32:17 2023] Finished job 2. 2 of 15 steps (13%) done Select jobs to execute...

[Mon Dec 11 22:32:19 2023] rule plddt: input: ./myfam/finalset.csv output: ./myfam/plddt.json log: ./myfam/logs/plddt.log jobid: 1 reason: Missing output files: ./myfam/plddt.json; Input files updated by another job: ./myfam/finalset.csv wildcards: folder=./myfam resources: tmpdir=/tmp

[Mon Dec 11 22:32:19 2023] rule foldseek_allvall_1: input: ./myfam/finalset.csv output: ./myfam/allvall_1.csv log: ./myfam/logs/foldseekallvall.log jobid: 8 reason: Missing output files: ./myfam/allvall_1.csv; Input files updated by another job: ./myfam/finalset.csv wildcards: folder=./myfam resources: tmpdir=/tmp

Activating conda environment: foldtree Activating conda environment: foldtree Create directory ./myfam/tmp easy-search ./myfam/structs/ ./myfam/structs/ ./myfam/allvall_1.csv ./myfam/tmp --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,lddt,lddtfull,alntmscore --exhaustive-search --alignment-type 2 -e inf --threads 4

MMseqs Version: 30fdcac78217579fa25d59bc271bd4f3767d3ebb Seq. id. threshold 0 Coverage threshold 0 Coverage mode 0 Max reject 2147483647 Max accept 2147483647 Add backtrace false TMscore threshold 0 TMalign hit order 0 TMalign fast 1 Preload mode 0 Threads 4 Verbosity 3 LDDT threshold 0 Sort by structure bit score 1 Substitution matrix aa:3di.out,nucl:3di.out Alignment mode 3 Alignment mode 0 E-value threshold inf Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Max sequence length 65535 Compositional bias 1 Compositional bias 1 Gap open cost aa:10,nucl:10 Gap extension cost aa:1,nucl:1 Compressed 0 Seed substitution matrix aa:3di.out,nucl:3di.out Sensitivity 9.5 k-mer length 6 k-score seq:2147483647,prof:2147483647 Max results per query 1000 Split database 0 Split mode 2 Split memory limit 0 Diagonal scoring true Exact k-mer matching 0 Mask residues 0 Mask residues probability 0.99995 Mask lower case residues 1 Minimum diagonal score 15 Selected taxa
Spaced k-mers 1 Spaced k-mer pattern
Local temporary path
Exhaustive search mode true Search iterations 1 Alignment type 2 Remove temporary files true MPI runner
Force restart with latest tmp false Chain name mode 0 Mask b-factor threshold 0 Coord store mode 2 Write lookup file 1 Tar Inclusion Regex .* Tar Exclusion Regex ^$ Alignment format 0 Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,lddt,lddtfull,alntmscore Database output false

Alignment backtraces will be computed, since they were requested by output format. Activating conda environment: foldtree createdb ./myfam/structs/ ./myfam/tmp/8403657280465428595/query --chain-name-mode 0 --mask-bfactor-threshold 0 --coord-store-mode 2 --write-lookup 1 --tar-include '.*' --tar-exclude '^$' --threads 4 -v 3

Output file: ./myfam/tmp/8403657280465428595/query [=================================================================] 100.00% 4 0s 5ms
Time for merging to query_ss: 0h 0m 0s 25ms ] 0.00% 1 eta -0s
Time for merging to query_h: 0h 0m 0s 24ms Time for merging to query_ca: 0h 0m 0s 24ms Time for merging to query: 0h 0m 0s 25ms Ignore 0 out of 4. Too short: 0, incorrect 0. Time for processing: 0h 0m 0s 277ms createdb ./myfam/structs/ ./myfam/tmp/8403657280465428595/target --chain-name-mode 0 --mask-bfactor-threshold 0 --coord-store-mode 2 --write-lookup 1 --tar-include '.*' --tar-exclude '^$' --threads 4 -v 3

Output file: ./myfam/tmp/8403657280465428595/target [=================================================================] 100.00% 4 0s 2ms
Time for merging to target_ss: 0h 0m 0s 25ms ] 33.33% 2 eta 0s
Time for merging to target_h: 0h 0m 0s 22ms Time for merging to target_ca: 0h 0m 0s 21ms Time for merging to target: 0h 0m 0s 22ms Ignore 0 out of 4. Too short: 0, incorrect 0. Time for processing: 0h 0m 0s 247ms Create directory ./myfam/tmp/8403657280465428595/search_tmp search ./myfam/tmp/8403657280465428595/query ./myfam/tmp/8403657280465428595/target ./myfam/tmp/8403657280465428595/result ./myfam/tmp/8403657280465428595/search_tmp -a 1 --threads 4 --alignment-mode 3 -e inf --comp-bias-corr 1 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 -s 9.5 -k 6 --mask 0 --mask-prob 0.99995 --exhaustive-search 1 --alignment-type 2 --remove-tmp-files 1

structurealign ./myfam/tmp/8403657280465428595/query ./myfam/tmp/8403657280465428595/target ./myfam/tmp/8403657280465428595/search_tmp/12563776430131480020/pref ./myfam/tmp/8403657280465428595/search_tmp/12563776430131480020/aln --tmscore-threshold 0 --lddt-threshold 0 --sort-by-structure-bits 1 --sub-mat 'aa:3di.out,nucl:3di.out' -a 1 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e inf --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 0.5 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 --zdrop 40 --threads 4 --compressed 0 -v 3

[=================================================================] 100.00% 4 0s 55ms
Time for merging to aln: 0h 0m 0s 15ms Time for processing: 0h 0m 0s 229ms mvdb ./myfam/tmp/8403657280465428595/search_tmp/12563776430131480020/aln ./myfam/tmp/8403657280465428595/result -v 3

Time for processing: 0h 0m 0s 44ms Removing temporary files rmdb ./myfam/tmp/8403657280465428595/search_tmp/12563776430131480020/pref -v 3

Time for processing: 0h 0m 0s 12ms convertalis ./myfam/tmp/8403657280465428595/query ./myfam/tmp/8403657280465428595/target ./myfam/tmp/8403657280465428595/result ./myfam/allvall_1.csv --sub-mat 'aa:3di.out,nucl:3di.out' --format-mode 0 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,lddt,lddtfull,alntmscore --translation-table 1 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 --db-output 0 --db-load-mode 0 --search-type 0 --threads 4 --compressed 0 -v 3

[=================================================================] 100.00% 4 0s 260ms
Time for merging to allvall_1.csv: 0h 0m 0s 16ms Time for processing: 0h 0m 0s 375ms rmdb ./myfam/tmp/8403657280465428595/result -v 3

Time for processing: 0h 0m 0s 14ms rmdb ./myfam/tmp/8403657280465428595/target -v 3

Time for processing: 0h 0m 0s 10ms rmdb ./myfam/tmp/8403657280465428595/target_h -v 3

Time for processing: 0h 0m 0s 5ms rmdb ./myfam/tmp/8403657280465428595/target_ca -v 3

Time for processing: 0h 0m 0s 5ms rmdb ./myfam/tmp/8403657280465428595/target_ss -v 3

Time for processing: 0h 0m 0s 7ms rmdb ./myfam/tmp/8403657280465428595/query -v 3

Time for processing: 0h 0m 0s 10ms rmdb ./myfam/tmp/8403657280465428595/query_h -v 3

Time for processing: 0h 0m 0s 6ms rmdb ./myfam/tmp/8403657280465428595/query_ca -v 3

Time for processing: 0h 0m 0s 7ms rmdb ./myfam/tmp/8403657280465428595/query_ss -v 3

Time for processing: 0h 0m 0s 8ms [Mon Dec 11 22:32:22 2023] Finished job 8. 3 of 15 steps (20%) done Select jobs to execute...

[Mon Dec 11 22:32:22 2023] rule foldseek2distmat: input: ./myfam/allvall_1.csv output: ./myfam/foldtree_fastmemat.txt, ./myfam/alntmscore_fastmemat.txt, ./myfam/lddt_fastmemat.txt log: ./myfam/logs/foldseek2distmat.log jobid: 7 reason: Missing output files: ./myfam/lddt_fastmemat.txt, ./myfam/foldtree_fastmemat.txt, ./myfam/alntmscore_fastmemat.txt; Input files updated by another job: ./myfam/allvall_1.csv wildcards: folder=./myfam resources: tmpdir=/tmp

Activating conda environment: foldtree Activating conda environment: foldtree [Mon Dec 11 22:32:25 2023] Finished job 1. 4 of 15 steps (27%) done Traceback (most recent call last): File "/work/home/ac1daawz21/software/fold_tree/.snakemake/scripts/tmp204w6d1r.foldseekres2distmat_simple.py", line 5, in import foldseek2tree File "/work/home/ac1daawz21/software/fold_tree/workflow/../src/foldseek2tree.py", line 6, in import toytree File "/work/home/ac1daawz21/miniconda3/envs/foldtree/lib/python3.10/site-packages/toytree/init.py", line 6, in from .Toytree import ToyTree as tree File "/work/home/ac1daawz21/miniconda3/envs/foldtree/lib/python3.10/site-packages/toytree/Toytree.py", line 11, in from .TreeStyle import TreeStyle, COLORS2 File "/work/home/ac1daawz21/miniconda3/envs/foldtree/lib/python3.10/site-packages/toytree/TreeStyle.py", line 14, in COLORS1 = [toyplot.color.to_css(i) for i in toyplot.color.brewer.palette("Set2")] AttributeError: 'function' object has no attribute 'palette'. Did you mean: 'palettes'? [Mon Dec 11 22:32:27 2023] Error in rule foldseek2distmat: jobid: 7 input: ./myfam/allvall_1.csv output: ./myfam/foldtree_fastmemat.txt, ./myfam/alntmscore_fastmemat.txt, ./myfam/lddt_fastmemat.txt log: ./myfam/logs/foldseek2distmat.log (check log file(s) for error details) conda-env: foldtree

RuleException: CalledProcessError in file /work/home/ac1daawz21/software/fold_tree/workflow/fold_tree, line 90: Command 'source /work/home/ac1daawz21/miniconda3/bin/activate 'foldtree'; set -euo pipefail; python /work/home/ac1daawz21/software/fold_tree/.snakemake/scripts/tmp204w6d1r.foldseekres2distmat_simple.py' returned non-zero exit status 1. File "/work/home/ac1daawz21/software/fold_tree/workflow/fold_tree", line 90, in __rule_foldseek2distmat File "/work/home/ac1daawz21/miniconda3/envs/foldtree/lib/python3.10/concurrent/futures/thread.py", line 58, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-12-11T223041.982368.snakemake.log

cactuskid commented 11 months ago

hey. This looks like a toytree error when it tries to import toyplot. Can you try activating the foldtree environment on the command line using mamba and reinstalling the toytree and toyplot packages with this command: pip install --upgrade --force-reinstall toytree toyplot . Normally they should be installed correctly when creating the environment but something might have gone wrong.

BinhongLiu commented 11 months ago

It worked. Thanks!

cactuskid commented 11 months ago

happy treebuilding!