Comments (5)
splaisan
commented on July 23, 2024
1
I will first thing monday and post here. I will also rebuild a conda using the new conda version which now finally uses mamba_lib to search for packages (was about time they switched). This only has fixed another issue I had this week.
Good WE!
from bakta.
splaisan
commented on July 23, 2024
1
Hi @oschwengers,
I tried it once more with my existing env to confirm it fails (it did)
I deleted my conda and created a new one with conda 23.
It now works through 'predict & annotate CDSs...' and end with all expected results
It confirms that the new conda 23.10.0 with mamba resole did build a good environment
problem solved for me
thanks for your support
I reproduce here the last failed run and list of packages as well as the new list of packages in case that can help you figure out who was guilty. I strongly suspect pyrodigal 2.3 now instead of 3.10 before !
conda previous bad env
bakta --db /data/biodata/bakta_db/db --genus "${genus}" --species "${species}" --strain "${strain}" --prefix "bc${bc}" --complete --output out bc01_assembly.fasta
parse genome sequences...
imported: 3
filtered & revised: 3
chromosomes: 1
plasmids: 2
start annotation...
predict tRNAs...
found: 74
predict tmRNAs...
found: 1
predict rRNAs...
found: 18
predict ncRNAs...
found: 34
predict ncRNA regions...
found: 7
predict CRISPR arrays...
found: 2
predict & annotate CDSs...
Traceback (most recent call last):
File "/opt/miniconda3/envs/bakta/bin/bakta", line 10, in <module>
sys.exit(main())
File "/opt/miniconda3/envs/bakta/lib/python3.10/site-packages/bakta/main.py", line 228, in main
cdss = feat_cds.predict(genome, contigs_path)
File "/opt/miniconda3/envs/bakta/lib/python3.10/site-packages/bakta/features/cds.py", line 41, in predict
orffinder = pyrodigal.OrfFinder(meta=prodigal_metamode, closed=closed)
AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'
(bakta) $ conda list
# packages in environment at /opt/miniconda3/envs/bakta:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
about-time 4.2.1 pyhd8ed1ab_0 conda-forge
alive-progress 3.0.1 pyhd8ed1ab_0 conda-forge
aragorn 1.2.41 h031d066_1 bioconda
archspec 0.2.1 pyhd8ed1ab_1 conda-forge
bakta 1.8.2 pyhdfd78af_0 bioconda
biopython 1.81 py310h2372a71_1 conda-forge
blast 2.14.0 h7d5a4b4_1 bioconda
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.20.1 hd590300_1 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py310h2fee648_0 conda-forge
charset-normalizer 3.3.1 pyhd8ed1ab_0 conda-forge
circos 0.69.9 hdfd78af_0 bioconda
curl 8.4.0 hca28451_0 conda-forge
diamond 2.1.8 h43eeafb_0 bioconda
entrez-direct 16.2 he881be0_1 bioconda
expat 2.5.0 hcb278e6_1 conda-forge
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 hab24e00_0 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
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
grapheme 0.6.0 pyhd8ed1ab_0 conda-forge
hmmer 3.3.2 hdbdd923_4 bioconda
icu 73.2 h59595ed_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
infernal 1.1.4 pl5321h031d066_4 bioconda
isa-l 2.30.0 hd590300_6 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 19_linux64_openblas conda-forge
libcblas 3.9.0 19_linux64_openblas conda-forge
libcurl 8.4.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgfortran-ng 13.2.0 h69a702a_2 conda-forge
libgfortran5 13.2.0 ha4646dd_2 conda-forge
libgomp 13.2.0 h807b86a_2 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 19_linux64_openblas conda-forge
libnghttp2 1.55.1 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsqlite 3.43.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.3.2 h658648e_1 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
ncbi-amrfinderplus 3.11.26 h283d18e_0 bioconda
ncurses 6.4 h59595ed_1 conda-forge
numpy 1.26.0 py310hb13e2d6_0 conda-forge
openssl 3.1.4 hd590300_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 4_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-b-cow 0.007 pl5321h166bdaf_0 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-clone 0.46 pl5321h166bdaf_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge
perl-config-general 2.65 pl5321hdfd78af_0 bioconda
perl-digest-perl-md5 1.9 pl5321hdfd78af_2 bioconda
perl-encode 3.19 pl5321h166bdaf_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-config 0.008 pl5321ha770c72_0 conda-forge
perl-extutils-helpers 0.026 pl5321ha770c72_0 conda-forge
perl-extutils-installpaths 0.012 pl5321ha770c72_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-extutils-pl2bat 0.005 pl5321ha770c72_0 conda-forge
perl-font-ttf 1.06 pl5321hdfd78af_1 bioconda
perl-gd 2.76 pl5321h5b5514e_1 bioconda
perl-inc-latest 0.500 pl5321ha770c72_0 conda-forge
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-math-bezier 0.01 pl5321hdfd78af_2 bioconda
perl-math-round 0.07 pl5321ha770c72_0 conda-forge
perl-math-vecstat 0.08 pl5321hdfd78af_2 bioconda
perl-module-build 0.4232 pl5321ha770c72_0 conda-forge
perl-module-build-tiny 0.039 pl5321h166bdaf_0 conda-forge
perl-module-implementation 0.09 pl5321ha770c72_0 conda-forge
perl-module-runtime 0.016 pl5321ha770c72_0 conda-forge
perl-number-format 1.76 pl5321hdfd78af_0 bioconda
perl-params-validate 1.31 pl5321hec16e2b_0 bioconda
perl-parent 0.241 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-readonly 2.05 pl5321ha770c72_0 conda-forge
perl-regexp-common 2017060201 pl5321hd8ed1ab_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-set-intspan 1.19 pl5321hdfd78af_2 bioconda
perl-statistics-basic 1.6611 pl5321hdfd78af_3 bioconda
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-svg 2.87 pl5321hd8ed1ab_0 conda-forge
perl-test-fatal 0.016 pl5321ha770c72_0 conda-forge
perl-text-format 0.62 pl5321hdfd78af_0 bioconda
perl-time-hires 1.9764 pl5321h031d066_4 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge
pigz 2.8 h2797004_0 conda-forge
piler-cr 1.06 h4ac6f70_4 bioconda
pip 23.3.1 pyhd8ed1ab_0 conda-forge
psutil 5.9.5 py310h2372a71_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyhmmer 0.10.4 py310h4b81fae_0 bioconda
pyrodigal 3.1.0 py310h4b81fae_0 bioconda
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.13 hd12c33a_0_cpython conda-forge
python-isal 1.5.1 py310h2372a71_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pyyaml 6.0.1 py310h2372a71_1 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h2797004_0 conda-forge
trnascan-se 2.0.12 pl5321h031d066_0 bioconda
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.0.7 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha35d2d1_1 conda-forge
wheel 0.41.3 pyhd8ed1ab_0 conda-forge
xopen 1.8.0 py310hff52083_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.21.0 py310h1275a96_1 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
conda 23.0.1 new working env
# packages in environment at /opt/miniconda3/envs/bakta:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
about-time 4.2.1 pyhd8ed1ab_0 conda-forge
alive-progress 3.0.1 pyhd8ed1ab_0 conda-forge
aragorn 1.2.41 h031d066_1 bioconda
archspec 0.2.2 pyhd8ed1ab_0 conda-forge
bakta 1.8.2 pyhdfd78af_1 bioconda
biopython 1.81 py310h2372a71_1 conda-forge
blast 2.15.0 pl5321h6f7f691_1 bioconda
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.21.0 hd590300_0 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py310h2fee648_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
circos 0.69.9 hdfd78af_0 bioconda
curl 8.4.0 hca28451_0 conda-forge
diamond 2.1.8 h43eeafb_0 bioconda
entrez-direct 16.2 he881be0_1 bioconda
expat 2.5.0 hcb278e6_1 conda-forge
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 hab24e00_0 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
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
grapheme 0.6.0 pyhd8ed1ab_0 conda-forge
hmmer 3.3.2 hdbdd923_4 bioconda
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
infernal 1.1.4 pl5321h031d066_4 bioconda
isa-l 2.30.0 hd590300_6 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 19_linux64_openblas conda-forge
libcblas 3.9.0 19_linux64_openblas conda-forge
libcurl 8.4.0 hca28451_0 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 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
libgd 2.3.3 h5aea950_4 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
liblapack 3.9.0 19_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsqlite 3.44.0 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.2.4 h1daa5a0_1 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxml2 2.9.14 h22db469_4 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
ncbi-amrfinderplus 3.11.26 h283d18e_0 bioconda
ncbi-vdb 3.0.8 hdbdd923_0 bioconda
ncurses 6.4 h59595ed_2 conda-forge
numpy 1.26.0 py310hb13e2d6_0 conda-forge
openssl 3.1.4 hd590300_0 conda-forge
ossuuid 1.6.2 hf484d3e_1000 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 4_hd590300_perl5 conda-forge
perl-alien-build 2.48 pl5321hec16e2b_0 bioconda
perl-alien-libxml2 0.17 pl5321hec16e2b_0 bioconda
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-b-cow 0.007 pl5321h166bdaf_0 conda-forge
perl-business-isbn 3.007 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn-data 20210112.006 pl5321hd8ed1ab_0 conda-forge
perl-capture-tiny 0.48 pl5321ha770c72_1 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-clone 0.46 pl5321h166bdaf_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge
perl-config-general 2.65 pl5321hdfd78af_0 bioconda
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-digest-perl-md5 1.9 pl5321hdfd78af_2 bioconda
perl-encode 3.19 pl5321h166bdaf_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-config 0.008 pl5321ha770c72_0 conda-forge
perl-extutils-helpers 0.026 pl5321ha770c72_0 conda-forge
perl-extutils-installpaths 0.012 pl5321ha770c72_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-extutils-pl2bat 0.005 pl5321ha770c72_0 conda-forge
perl-ffi-checklib 0.28 pl5321hdfd78af_0 bioconda
perl-file-chdir 0.1011 pl5321hd8ed1ab_0 conda-forge
perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge
perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge
perl-file-which 1.24 pl5321hd8ed1ab_0 conda-forge
perl-font-ttf 1.06 pl5321hdfd78af_1 bioconda
perl-gd 2.76 pl5321h5b5514e_1 bioconda
perl-importer 0.026 pl5321hd8ed1ab_0 conda-forge
perl-inc-latest 0.500 pl5321ha770c72_0 conda-forge
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-math-bezier 0.01 pl5321hdfd78af_2 bioconda
perl-math-round 0.07 pl5321ha770c72_0 conda-forge
perl-math-vecstat 0.08 pl5321hdfd78af_2 bioconda
perl-module-build 0.4234 pl5321ha770c72_0 conda-forge
perl-module-build-tiny 0.039 pl5321h166bdaf_0 conda-forge
perl-module-implementation 0.09 pl5321ha770c72_0 conda-forge
perl-module-runtime 0.016 pl5321hdfd78af_2 bioconda
perl-number-format 1.76 pl5321hdfd78af_0 bioconda
perl-params-validate 1.31 pl5321h031d066_2 bioconda
perl-parent 0.241 pl5321hd8ed1ab_0 conda-forge
perl-path-tiny 0.124 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-readonly 2.05 pl5321ha770c72_0 conda-forge
perl-regexp-common 2017060201 pl5321hd8ed1ab_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-scope-guard 0.21 pl5321hd8ed1ab_0 conda-forge
perl-set-intspan 1.19 pl5321hdfd78af_2 bioconda
perl-statistics-basic 1.6611 pl5321hdfd78af_3 bioconda
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-sub-info 0.002 pl5321hd8ed1ab_0 conda-forge
perl-svg 2.87 pl5321hd8ed1ab_0 conda-forge
perl-term-table 0.016 pl5321hdfd78af_0 bioconda
perl-test-fatal 0.016 pl5321ha770c72_0 conda-forge
perl-test-warnings 0.031 pl5321ha770c72_0 conda-forge
perl-test2-suite 0.000145 pl5321hdfd78af_0 bioconda
perl-text-format 0.62 pl5321hdfd78af_0 bioconda
perl-time-hires 1.9764 pl5321h031d066_4 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-uri 5.17 pl5321ha770c72_0 conda-forge
perl-xml-libxml 2.0207 pl5321h661654b_0 bioconda
perl-xml-namespacesupport 1.12 pl5321hd8ed1ab_0 conda-forge
perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge
perl-xml-sax 1.02 pl5321hd8ed1ab_0 conda-forge
perl-xml-sax-base 1.09 pl5321hd8ed1ab_0 conda-forge
pigz 2.8 h2797004_0 conda-forge
piler-cr 1.06 h4ac6f70_4 bioconda
pip 23.3.1 pyhd8ed1ab_0 conda-forge
psutil 5.9.5 py310h2372a71_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyhmmer 0.10.4 py310h4b81fae_0 bioconda
pyrodigal 2.3.0 py310h4b81fae_1 bioconda
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.13 hd12c33a_0_cpython conda-forge
python-isal 1.5.2 py310h2372a71_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pyyaml 6.0.1 py310h2372a71_1 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
trnascan-se 2.0.12 pl5321h031d066_0 bioconda
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.0.7 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha35d2d1_1 conda-forge
wheel 0.41.3 pyhd8ed1ab_0 conda-forge
xopen 1.8.0 py310hff52083_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.22.0 py310h1275a96_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
from bakta.
oschwengers
commented on July 23, 2024
1
You're welcome. Glad that it's now working. FYI, upcoming Bakta v1.9.0 will actually use Pyrodigal >= v3.1.0.
from bakta.
splaisan
commented on July 23, 2024
I reinstalled with conda from scratch once more with conda install -c conda-forge -c bioconda bakta pyrodigal=3.1.0 to hopefully get a better version with Pyrodigal and I do not get a Pyrodigal executable, just pyrodigal.
pyrodigal -V
pyrodigal v3.1.0
my command fails with:
ERROR: Pyrodigal could not be executed! Please make sure Pyrodigal is installed and executable or skip requiring workflow steps via via '--skip-cds'.
from bakta.
oschwengers
commented on July 23, 2024
Hi @splaisan,
thanks for reporting. First, to sort things a bit, Bakta actually checks for pyrodigal but uses the canonical tool name Pyrodigal for error messaging. There are more obvious cases like AMRFinderPlus which command is amrfinder.
This having said, I currently do not understand why Bakta fails to recognize Pyrodigal. Could you maybe run Bakta in --debug mode and provide the log file?
from bakta.
Related Issues (20)
- CRISPR position doesn't include last spacer
- circos legend HOT 1
- Reduce locus_tag offset from 5 to 1
- Color coding in bakta_plot --type cog HOT 2
- Inquiry about the coding density equation HOT 4
- Bakta run times on cluster HOT 4
- Downgrading dependencies is needed when installing bakta from conda HOT 2
- Roary is not working with bakta-generated gff3-files HOT 1
- KEGG annotations - the number is much lower number than expected HOT 4
- Possible issues running bakta in Singularity HOT 1
- Name and Product don't match Dbxref HOT 3
- Make the --region parameter better match the output of PGAP HOT 8
- tRNAscan-SE slow with multiple threads HOT 3
- PSC failed! diamond-error-code=-11 HOT 2
- Bakta Web Does Not Work HOT 6
- Diamond Error -9 HOT 3
- Is there a way to deactivate the overlap detection so bakta does not filter my input proteins? HOT 3
- Inquiry on CDS annotation HOT 2
- pyhmmer not found HOT 14
- pyrodigal has no attribute 'OrfFinder' HOT 11
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bakta.