Installation Issue macOS BigSur

[ftettamanti]

Hi,

I am trying to install tormes but when I use: conda env create -n tormes-1.3.0 --file tormes-1.3.0.yml, I get the following error:

Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

• ant=1.10.0
• mauvealigner=1.2.0
• tormes=1.3.0

I have updated conda but it has not resolved the issue. Any help much appreciated.

Thanks!

[nmquijada]

Hi @ftettamanti

It seems that you have issues with some dependencies of tormes that ultimately makes its installation to fail.
Never tried with a macOS BigSur (thanks for specifying!), but we will find a way.

Just to make sure that there are not non-used incompatible dependencies, I suggest to remove the environment and perform a clean up:

conda env remove -n tormes-1.3.0
conda update conda
conda clean --all

After that, try to install tormes again: conda env create -n tormes-1.3.0 --file tormes-1.3.0.yml

Let me know if it worked. If not, we will try a different installation.

Best,
Narciso

[vincenzopennone]

Hi,
I'm facing exactly the same issue, unfortunately removing tormes and cleaning didn't change anything.
Conda is updated, but nothing...
Any help is much appreciated!
Thanks
Vincenzo

[nmquijada]

Hi Vincenzo,

Sure, we'll find a way.
You are having troubles with ant and mauvealigner dependencies on that specific version. Tormes installation fails as it requires all the dependencies included in the yml file to be installed.

So, assuming that you have the tormes-1.3.0.yml file, please use this commands to removed from such files the conflict dependencies:
grep -E -v "ant=1.10.0|mauvealigner=1.2.0|tormes=1.3.0" tormes-1.3.0.yml > myenv.yml

Then, make a new conda environment (make sure to have the cleaning and updating done) and install the ant and mauvealigner dependencies without being strict with their versions:

conda env create -n tormes-1.3.0 --file myenv.yml
conda activate tormes-1.3.0
conda install -c bioconda ant mauvealigner

If it worked, you should be able to install the tormes conda package:

conda install -c nmquijada tormes

Please let me know if it worked or the errors your encountered, in case.

Narciso

[vincenzopennone]

Hi Narciso,

Thank you very much for your fast reply!
I used the grep command as you suggested on the .yml file, but when I tried to create the conda environment with the new .yml file... this happened (See below)... a lot of conflicts!
Should I burn my mac? I'm new to the terminal command lines... sorry if I made some mistakes...

Here is what I see in the terminal:

(base) vincenzopennone@MacBook-Pro-di-vincenzo ~ % conda env create -n tormes-1.3.0 --file myenv.yml

Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Examining conflict for r-biocmanager mauve imagemagick r-dt r-plotly r-stringi r-rmarkdown r-essentials quast r-base: : 51it [01:56, 3.41s/itExamining conflict for r-biocmanager mauve imagemagick r-dt r-plotly r-stringi r-rmarkdown r-essentials quast r-base: : 52it [01:56, 2.58s/i-Examining conflict for r-biocmanager r-dt sistr_cmd r-stringi r-rmarkdown r-essentials r-plotly r-base: : 52it [01:58, 2.58s/it] Examining conflict for r-biocmanager kraken2 mauve imagemagick r-dt r-stringi r-rmarkdown r-essentials git r-plotly r-base: : 53it [02:00, 2.Examining conflict for r-biocmanager kraken2 mauve imagemagick r-dt r-stringi r-rmarkdown r-essentials git r-plotly r-base: : 54it [02:00, 2.Examining conflict for r-biocmanager mauve imagemagick r-dt r-stringi r-rmarkdown r-essentials git r-plotly r-base: : 54it [02:03, 2.52s/it] Examining conflict for prokka abricate r-dt sistr_cmd roary r-plotly r-rmarkdown r-essentials fasttree quast barrnap: : 56it [02:07, 2.42s/itExamining conflict for prokka abricate r-dt sistr_cmd roary r-plotly r-rmarkdown r-essentials fasttree quast barrnap: : 57it [02:07, 2.36s/i|Examining conflict for python r-base: : 57it [02:10, 2.36s/it] failed
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Examining conflict for r-biocmanager mauve imagemagick r-dt r-plotly r-stringi r-rmarkdown r-essentials quast r-base: : 51it [02:01, 3.60s/itExamining conflict for r-biocmanager mauve imagemagick r-dt r-plotly r-stringi r-rmarkdown r-essentials quast r-base: : 52it [02:01, 2.72s/i|Examining conflict for r-biocmanager r-dt sistr_cmd r-stringi r-rmarkdown r-essentials r-plotly r-base: : 52it [02:04, 2.72s/it] Examining conflict for r-biocmanager kraken2 mauve imagemagick r-dt r-stringi r-rmarkdown r-essentials git r-plotly r-base: : 53it [02:06, 2.Examining conflict for r-biocmanager kraken2 mauve imagemagick r-dt r-stringi r-rmarkdown r-essentials git r-plotly r-base: : 54it [02:06, 2.Examining conflict for r-biocmanager mauve imagemagick r-dt r-stringi r-rmarkdown r-essentials git r-plotly r-base: : 54it [02:08, 2.59s/it] Examining conflict for prokka abricate r-dt sistr_cmd roary r-plotly r-rmarkdown r-essentials fasttree quast barrnap: : 56it [02:13, 2.51s/itExamining conflict for prokka abricate r-dt sistr_cmd roary r-plotly r-rmarkdown r-essentials fasttree quast barrnap: : 57it [02:13, 2.46s/i/Examining conflict for python r-base: : 57it [02:16, 2.46s/it] failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libiconv conflicts for:
mauve=2.4.0 -> fontconfig -> libiconv[version='1.15|>=1.15,<1.17.0a0|>=1.16,<1.17.0a0|>=1.15,<2.0a0']
imagemagick=7.0.10_28 -> fontconfig[version='>=2.13.1,<3.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.16,<1.17.0a0|>=1.16,<2.0a0|>=1.15,<2.0a0']
git=2.28.0 -> libiconv[version='>=1.15,<1.17.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.16,<1.17.0a0|>=1.15,<2.0a0']
git=2.28.0 -> gettext[version='>=0.19.8.1,<1.0a0'] -> libiconv[version='>=1.15,<2.0a0|>=1.16,<1.17.0a0|>=1.16,<2.0a0']
r-base=3.6.3 -> libiconv[version='>=1.15,<1.17.0a0|>=1.16,<1.17.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.15,<2.0a0|>=1.16,<1.17.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.16,<1.17.0a0|>=1.15,<2.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.16,<1.17.0a0|>=1.15,<2.0a0']
kraken2=2.0.9beta -> rsync -> libiconv[version='>=1.16,<1.17.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.16,<1.17.0a0|>=1.15,<2.0a0']
r-base=3.6.3 -> libxml2[version='>=2.9.12,<2.10.0a0'] -> libiconv[version='>=1.16,<2.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> libiconv[version='>=1.15,<1.17.0a0|>=1.15,<2.0a0|>=1.16,<1.17.0a0']

Package zlib conflicts for:
prokka=1.14.6 -> blast[version='>=2.7.1'] -> zlib[version='1.2.11.|>=1.2.11,<1.3.0a0|1.2.8.']
tabulate=0.8.7 -> python -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.']
barrnap=0.9 -> bedtools -> zlib[version='1.2.11.|>=1.2.11,<1.3.0a0|1.2.8.']
r-base=3.6.3 -> curl -> zlib[version='1.2.|1.2.11']
blast=2.10.1 -> zlib[version='>=1.2.11,<1.3.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> zlib[version='1.2.|1.2.11|1.2.11.|>=1.2.11,<1.3.0a0|1.2.8.|1.2.8']
spades=3.15.2 -> python -> zlib[version='1.2.|1.2.11|1.2.8|1.2.11.']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> zlib[version='1.2.|1.2.11']
imagemagick=7.0.10_28 -> zlib[version='>=1.2.11,<1.3.0a0']
mlst=2.19.0 -> zlib
spades=3.15.2 -> zlib[version='>=1.2.11,<1.3.0a0']
r-base=3.6.3 -> zlib[version='>=1.2.11,<1.3.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
trimmomatic=0.39 -> openjdk -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.']
rdptools=2.0.3 -> python -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.']
quast=5.0.2 -> blast -> zlib[version='1.2.|1.2.11|1.2.11.|1.2.8.|1.2.8']
git=2.28.0 -> zlib[version='>=1.2.11,<1.3.0a0']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> zlib[version='>=1.2.11,<1.3.0a0']
sistr_cmd=1.1.1 -> blast -> zlib[version='1.2.|1.2.11|1.2.11.|>=1.2.11,<1.3.0a0|1.2.8.|1.2.8']
megahit=1.2.9 -> zlib[version='>=1.2.11,<1.3.0a0']
megahit=1.2.9 -> python -> zlib[version='1.2.|1.2.11|1.2.8|1.2.11.']
python=3.6.11 -> zlib[version='>=1.2.11,<1.3.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|1.2.8']
cgecore=1.5.6 -> python -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.']
sickle-trim=1.33 -> zlib[version='1.2.11.|>=1.2.11,<1.3.0a0|1.2.8']
quast=5.0.2 -> zlib[version='>=1.2.11,<1.3.0a0']
roary=3.13.0 -> bedtools -> zlib[version='1.2.11.|>=1.2.11,<1.3.0a0|1.2.8.']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
mauve=2.4.0 -> openjdk -> zlib[version='>=1.2.11,<1.3.0a0']
kraken2=2.0.9beta -> blast -> zlib[version='1.2.11|1.2.11.|>=1.2.11,<1.3.0a0|1.2.8.|1.2.8']
abricate=1.0.1 -> blast[version='>=2.7'] -> zlib[version='1.2.11.|1.2.8.*']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
abricate=1.0.1 -> zlib[version='>=1.2.11,<1.3.0a0']

Package llvm-openmp conflicts for:
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=8.0.1|>=8.0.0|>=4.0.1|>=11.0.1']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
abricate=1.0.1 -> blast[version='>=2.7'] -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
r-base=3.6.3 -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.1.0|>=9.0.1']
sistr_cmd=1.1.1 -> blast -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
blast=2.10.1 -> llvm-openmp[version='>=10.0.1|>=11.0.0']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
git=2.28.0 -> gettext[version='>=0.19.8.1,<1.0a0'] -> llvm-openmp[version='>=10.0.0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=4.0.1|>=8.0.0|>=8.0.1|>=9.0.1|>=12.0.1|>=9.0.0']
kraken2=2.0.9beta -> llvm-openmp[version='>=8.0.1']
r-base=3.6.3 -> libgfortran5[version='>=9.3.0'] -> llvm-openmp[version='10.0.0.*|>=10.0.1|>=8.0.0|>=8.0.1']
roary=3.13.0 -> blast -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=8.0.1']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=8.0.1|>=8.0.0|>=4.0.1|>=11.0.1']
megahit=1.2.9 -> llvm-openmp[version='>=8.0.1']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=8.0.1|>=8.0.0|>=4.0.1|>=12.0.1|>=11.0.1|>=10.0.1']
spades=3.15.2 -> llvm-openmp[version='>=11.1.0|>=9.0.1']
imagemagick=7.0.10_28 -> fftw[version='>=3.3.9,<4.0a0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=4.0.1|>=9.0.0|>=8.0.1|>=8.0.0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=8.0.1|>=8.0.0|>=4.0.1|>=11.0.1']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.1.0|>=4.0.1|>=8.0.0|>=8.0.1|>=9.0.1|>=9.0.0']
quast=5.0.2 -> blast -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
kraken2=2.0.9beta -> blast -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']

Package xz conflicts for:
r-base=3.6.3 -> libtiff[version='>=4.2.0,<5.0a0'] -> xz[version='>=5.2.4,<6.0a0|>=5.2.5,<6.0a0']
barrnap=0.9 -> bedtools -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
imagemagick=7.0.10_28 -> xz[version='>=5.2.5,<5.3.0a0']
roary=3.13.0 -> bedtools -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
cgecore=1.5.6 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
trimmomatic=0.39 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.4,<6.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0|>=5.2.5,<5.3.0a0']
python=3.6.11 -> xz[version='>=5.2.5,<5.3.0a0']
kaptive=0.7.3 -> python[version='>=3'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
megahit=1.2.9 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.4,<6.0a0']
quast=5.0.2 -> python[version='>=3.7,<3.8.0a0'] -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0|>=5.2.5,<5.3.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.4,<6.0a0']
sistr_cmd=1.1.1 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
r-base=3.6.3 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
rdptools=2.0.3 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.4,<6.0a0']
tabulate=0.8.7 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
spades=3.15.2 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']

Package libopenblas conflicts for:
biopython=1.77 -> numpy -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.3,<1.0a0']
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.3,<1.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.5,<3.6.0a0'] -> libopenblas[version='>=0.2.20,<0.2.21.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.5,<3.6.0a0'] -> libopenblas[version='>=0.2.20,<0.2.21.0a0']
kaptive=0.7.3 -> numpy -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.3,<1.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.5,<3.6.0a0'] -> libopenblas[version='>=0.2.20,<0.2.21.0a0']
r-base=3.6.3 -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas[version='>=0.3.10,<0.3.11.0a0|>=0.3.12,<0.3.13.0a0|>=0.3.15,<0.3.16.0a0|>=0.3.17,<0.3.18.0a0|>=0.3.17,<1.0a0|>=0.3.15,<1.0a0|>=0.3.12,<1.0a0|>=0.3.10,<1.0a0|>=0.3.9,<0.3.10.0a0|>=0.3.9,<1.0a0|>=0.3.8,<0.3.9.0a0|>=0.3.8,<1.0a0|>=0.3.7,<0.3.8.0a0|>=0.3.7,<1.0a0|>=0.3.6,<0.3.7.0a0|>=0.3.6,<1.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libopenblas[version='>=0.2.20,<0.2.21.0a0']

Package perl-lwp-simple conflicts for:
roary=3.13.0 -> perl-digest-md5-file -> perl-lwp-simple
blast=2.10.1 -> entrez-direct -> perl-lwp-simple
abricate=1.0.1 -> perl-lwp-simple

Package libgfortran4 conflicts for:
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-base=3.6.3 -> libgfortran4[version='>=7.5.0']
r-dt=0.5 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-plotly=4.9.0 -> r-hexbin -> libgfortran4[version='>=7.5.0']
imagemagick=7.0.10_28 -> fftw[version='>=3.3.8,<4.0a0'] -> libgfortran4[version='>=7.5.0']
sistr_cmd=1.1.1 -> scipy[version='>=1.1.0'] -> libgfortran4[version='>=7.5.0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran4[version='>=7.5.0']
r-base=3.6.3 -> libgfortran=4 -> libgfortran4

Package python conflicts for:
quast=5.0.2 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
imagemagick=7.0.10_28 -> glib[version='>=2.58.3,<3.0a0'] -> python[version='|>=2.7|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0']
spades=3.15.2 -> python
kaptive=0.7.3 -> biopython[version='<1.78'] -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.|>=3.9,<3.10.0a0']
tabulate=0.8.7 -> python[version='>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
sistr_cmd=1.1.1 -> python
rdptools=2.0.3 -> python
trimmomatic=0.39 -> python
megahit=1.2.9 -> python
cgecore=1.5.6 -> python
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|3.4.|>=3.6|>=3.7.1,<3.8.0a0']
python=3.6.11
kaptive=0.7.3 -> python[version='>=3']
quast=5.0.2 -> joblib -> python[version='2.7.|3.5.|3.6.|>=3.6|3.4.|>=3.5,<3.6.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|3.7.']
cgecore=1.5.6 -> biopython -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|3.4.']
r-essentials=3.6 -> notebook[version='>=5.7.2'] -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.7|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0']

Package sqlite conflicts for:
quast=5.0.2 -> python[version='>=3.7,<3.8.0a0'] -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.36.0,<4.0a0|>=3.31.1,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0|>=3.30.0,<4.0a0']
tabulate=0.8.7 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
sistr_cmd=1.1.1 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
cgecore=1.5.6 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
trimmomatic=0.39 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
spades=3.15.2 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
megahit=1.2.9 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
kaptive=0.7.3 -> python[version='>=3'] -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']
python=3.6.11 -> sqlite[version='>=3.32.3,<4.0a0|>=3.33.0,<4.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.29.0,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0|>=3.25.1,<4.0a0|>=3.27.2,<4.0a0']
rdptools=2.0.3 -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|3.9.|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0']

Package perl conflicts for:
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> perl[version='5.22.0.|>=5.26.2,<5.26.3.0a0']
perl-try-tiny=0.30 -> perl[version='>=5.26.2,<5.26.3.0a0']
kraken2=2.0.9beta -> perl[version='>=5.26.2,<5.26.3.0a0']
roary=3.13.0 -> blast -> perl[version='5.22.0.|>5.0.0|>=5.26.0,<5.27.0a0|>=5.26.2,<5.27.0a0']
quast=5.0.2 -> perl[version='>=5.26.2,<5.26.3.0a0']
mlst=2.19.0 -> perl
blast=2.10.1 -> entrez-direct -> perl[version='5.22.0.|>=5.26.0,<5.27.0a0|>=5.26.2,<5.27.0a0']
prinseq=0.20.4 -> perl
kraken2=2.0.9beta -> blast -> perl=5.22.0
bioconda::perl-try-tiny-retry=0.004 -> perl[version='>=5.26.2,<5.26.3.0a0']
blast=2.10.1 -> perl[version='>=5.26.2,<5.26.3.0a0']
barrnap=0.9 -> perl[version='>=5.22.0']
quast=5.0.2 -> blast -> perl=5.22.0
perl-data-dumper=2.173 -> perl[version='>=5.26.2,<5.26.3.0a0']
sistr_cmd=1.1.1 -> blast -> perl[version='5.22.0.|>=5.26.2,<5.26.3.0a0']
bioconda::perl-try-tiny-retry=0.004 -> perl-try-tiny -> perl[version='5.22.0.|>=5.26.2,<5.27.0a0']
roary=3.13.0 -> perl[version='>=5.26.2,<5.26.3.0a0']
abricate=1.0.1 -> any2fasta -> perl[version='5.22.0.|>=5.26.2,<5.26.3.0a0|>=5.26.0,<5.27.0a0|>=5.26.2,<5.27.0a0']
parallel=20200722 -> perl
mlst=2.19.0 -> blast[version='>=2.9.0'] -> perl[version='5.22.0.|>=5.26.0,<5.27.0a0|>=5.26.2,<5.26.3.0a0|>=5.26.2,<5.27.0a0']
imagemagick=7.0.10_28 -> perl[version='>=5.26.2,<5.26.3.0a0']
prokka=1.14.6 -> barrnap[version='>=0.7'] -> perl[version='5.22.0.|5.22.0|>=5.22.0|>5.0.0|>=5.26.0,<5.27.0a0']
prokka=1.14.6 -> perl[version='>=5.26.2,<5.26.3.0a0']
git=2.28.0 -> perl[version='>=5.26.2,<5.26.3.0a0']

Package python_abi conflicts for:
r-essentials=3.6 -> notebook[version='>=5.7.2'] -> python_abi[version='3.6|3.6.|3.7.|3.9.|3.8.|3.7',build='_pypy37_pp73|_pypy36_pp73|_cp38|_cp36m|_cp37m|_cp39']
cgecore=1.5.6 -> biopython -> python_abi[version='3.6.|3.6|3.7|3.7.|3.8.|3.9.',build='_cp38|_cp36m|_cp37m|_pypy37_pp73|_pypy36_pp73|_cp39']
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> python_abi[version='2.7.|3.6|3.6.|3.7|3.7.|3.8.|3.9.',build='_cp27m|_cp36m|_cp38|_cp37m|_pypy37_pp73|_cp39|_pypy36_pp73']
tabulate=0.8.7 -> python -> python_abi[version='3.6|3.7',build='_pypy37_pp73|_pypy36_pp73']
quast=5.0.2 -> matplotlib-base -> python_abi[version='3.6|3.7|3.8.|3.9.',build='_cp38|_pypy37_pp73|_cp39|_pypy36_pp73']
biopython=1.77 -> python_abi[version='3.6|3.6.|3.8.|3.7.',build='_cp37m|_cp38|_cp36m|_pypy36_pp73']
kaptive=0.7.3 -> biopython[version='<1.78'] -> python_abi[version='3.6|3.6.|3.8.|3.7.|3.7|3.9.',build='_cp37m|_cp38|_cp36m|_pypy36_pp73|_pypy37_pp73|_cp39']
trimmomatic=0.39 -> python -> python_abi[version='3.6|3.7',build='_pypy37_pp73|_pypy36_pp73']
biopython=1.77 -> numpy -> python_abi[version='3.7|3.9.',build='_pypy37_pp73|_cp39']
rdptools=2.0.3 -> python -> python_abi[version='3.6|3.7',build='_pypy37_pp73|_pypy36_pp73']
quast=5.0.2 -> python_abi[version='2.7.|3.6.|3.7.',build='_cp37m|_cp36m|_cp27m']
spades=3.15.2 -> python -> python_abi[version='3.6|3.7',build='_pypy37_pp73|_pypy36_pp73']
imagemagick=7.0.10_28 -> glib[version='>=2.58.3,<3.0a0'] -> python_abi[version='2.7.|3.6|3.6.|3.8.|3.7.',build='_cp37m|_cp38|_cp36m|_pypy36_pp73|_cp27m']
megahit=1.2.9 -> python -> python_abi[version='3.6|3.7',build='_pypy37_pp73|*_pypy36_pp73']

Package freetype conflicts for:
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
mauve=2.4.0 -> fontconfig -> freetype[version='2.6.|2.7|2.7.|2.7|2.8.1|>=2.10.4,<3.0a0|>=2.9.1,<3.0a0|>=2.8.1,<2.9.0a0|>=2.9,<3.0a0|>=2.8,<2.9.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
r-base=3.6.3 -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
quast=5.0.2 -> matplotlib-base -> freetype[version='2.6.*|>=2.10.2,<3.0a0|>=2.10.4,<3.0a0|>=2.9.1,<3.0a0|>=2.8,<2.9.0a0']
r-base=3.6.3 -> pango[version='>=1.42.4,<1.43.0a0'] -> freetype[version='>=2.10.2,<3.0a0']
imagemagick=7.0.10_28 -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> freetype[version='>=2.10.4,<3.0a0|>=2.9.1,<3.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> freetype[version='>=2.10.2,<3.0a0|>=2.8,<2.9.0a0']

Package icu conflicts for:
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> icu[version='>=58.2,<59.0a0|>=68.1,<69.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
r-base=3.6.3 -> icu[version='>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=68.1,<69.0a0|>=67.1,<68.0a0']
r-base=3.6.3 -> cairo[version='>=1.16.0,<1.17.0a0'] -> icu[version='>=58.2,<59.0a0']
imagemagick=7.0.10_28 -> fontconfig[version='>=2.13.1,<3.0a0'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
mauve=2.4.0 -> fontconfig -> icu[version='58.*|>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
r-stringi=1.4.6 -> icu[version='>=64.2,<65.0a0|>=67.1,<68.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=68.1,<69.0a0|>=67.1,<68.0a0']

Package perl-list-moreutils-xs conflicts for:
abricate=1.0.1 -> perl-list-moreutils -> perl-list-moreutils-xs
mlst=2.19.0 -> perl-list-moreutils -> perl-list-moreutils-xs
blast=2.10.1 -> perl-list-moreutils -> perl-list-moreutils-xs

Package libgfortran conflicts for:
imagemagick=7.0.10_28 -> fftw[version='>=3.3.9,<4.0a0'] -> libgfortran[version='4.|5.|>=4.0.0,<5.0.0.a0|>=3.0.1,<4.0.0.a0']
r-base=3.6.3 -> libblas[version='>=3.8.0,<4.0a0'] -> libgfortran[version='>=3.0.1,<4.0.0.a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libgfortran[version='4.|5.|>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0|>=4.0.0,<5.0.0.a0|>=3.0.1']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran[version='4.|5.|>=4.0.0,<5.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0,<4.0.0.a0|>=3.0.1']
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> libgfortran[version='4.|5.|>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0.1|>=4.0.0,<5.0.0.a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran[version='4.|5.|>=4.0.0,<5.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0,<4.0.0.a0|>=3.0.1']
kaptive=0.7.3 -> numpy -> libgfortran[version='>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0.1']
fasttree=2.1.10 -> libgcc -> libgfortran==3.0.1
r-base=3.6.3 -> libgfortran[version='4.|5.|>=4.0.0,<5.0.0.a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran[version='4.|5.|>=4.0.0,<5.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0,<4.0.0.a0|>=3.0.1']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> libgfortran[version='4.|5.|>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0|>=4.0.0,<5.0.0.a0|>=3.0.1']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libgfortran[version='4.|5.|>=4.0.0,<5.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0,<4.0.0.a0|>=3.0.1']
biopython=1.77 -> numpy -> libgfortran[version='>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0|>=3.0.1']

Package perl-threaded conflicts for:
abricate=1.0.1 -> perl-json -> perl-threaded
blast=2.10.1 -> entrez-direct -> perl-threaded
quast=5.0.2 -> circos -> perl-threaded
bioconda::perl-try-tiny-retry=0.004 -> perl-try-tiny -> perl-threaded
prokka=1.14.6 -> barrnap[version='>=0.7'] -> perl-threaded[version='>=5.22.0']
roary=3.13.0 -> mcl -> perl-threaded
mlst=2.19.0 -> perl-json -> perl-threaded

Package libcurl conflicts for:
git=2.28.0 -> curl[version='>=7.71.1,<8.0a0'] -> libcurl[version='7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.75.0|7.76.0|7.76.1|7.76.1|7.76.1|7.77.0|7.78.0|7.79.0|7.79.1|7.78.0',build='h8a08a2b_1|hb8e4fae_2|he6690cf_4|h9bf37e3_5|h9bf37e3_6|h8ef9fac_0|hf45b732_0|hf45b732_0|hf45b732_0|h97da3c1_1|hf45b732_1|hf45b732_0|hf45b732_2|h8ef9fac_1|h8ef9fac_0|h8ef9fac_0|h9bf37e3_8|he6690cf_1|he6690cf_0|hb8e4fae_0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libcurl[version='>=7.60.0,<8.0a0|>=7.61.0,<8.0a0|>=7.62.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.76.1,<8.0a0|>=7.78.0,<8.0a0|>=7.77.0,<8.0a0|>=7.71.0,<8.0a0|>=7.69.1,<8.0a0|>=7.67.0,<8.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libcurl[version='>=7.60.0,<8.0a0|>=7.61.0,<8.0a0|>=7.62.0,<8.0a0|>=7.64.1,<8.0a0|>=7.67.0,<8.0a0|>=7.76.1,<8.0a0|>=7.75.0,<8.0a0|>=7.71.1,<8.0a0']
sistr_cmd=1.1.1 -> pycurl[version='>=7.43.0'] -> libcurl[version='>=7.60.0,<8.0a0|>=7.63.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.77.0,<8.0a0|>=7.78.0,<8.0a0|>=7.67.0,<8.0a0|>=7.65.3,<8.0a0']
blast=2.10.1 -> curl[version='>=7.71.1,<8.0a0'] -> libcurl[version='7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.75.0|7.76.0|7.76.1|7.76.1|7.76.1|7.77.0|7.78.0|7.79.0|7.79.1|7.78.0',build='h8a08a2b_1|hb8e4fae_2|he6690cf_4|h9bf37e3_5|h9bf37e3_6|h8ef9fac_0|hf45b732_0|hf45b732_0|hf45b732_0|h97da3c1_1|hf45b732_1|hf45b732_0|hf45b732_2|h8ef9fac_1|h8ef9fac_0|h8ef9fac_0|h9bf37e3_8|he6690cf_1|he6690cf_0|hb8e4fae_0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> libcurl[version='>=7.61.0,<8.0a0|>=7.62.0,<8.0a0|>=7.64.1,<8.0a0|>=7.76.1,<8.0a0|>=7.75.0,<8.0a0|>=7.71.1,<8.0a0']
r-base=3.6.3 -> libcurl[version='>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.76.1,<8.0a0']
r-base=3.6.3 -> curl -> libcurl[version='7.57.0|7.58.0|7.59.0|7.60.0|7.61.0|7.61.1|7.61.1|7.61.1|7.62.0|7.62.0|7.63.0|7.63.0|7.64.0|7.64.0|7.64.0|7.64.0|7.64.1|7.64.1|7.65.2|7.65.3|7.68.0|7.68.0|7.69.1|7.71.0|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.71.1|7.75.0|7.76.0|7.76.1|7.76.1|7.76.1|7.77.0|7.78.0|7.79.0|7.79.1|7.78.0|7.71.1|7.71.1|7.71.0|7.69.1|7.68.0|7.67.0|7.65.3|7.65.2|7.64.1|7.64.0|7.63.0|7.63.0|7.62.0',build='hf30b1f0_0|hf30b1f0_0|hf30b1f0_0|hf30b1f0_0|hf30b1f0_0|hf30b1f0_0|h051b688_2|h8a08a2b_0|h8a08a2b_1|h76de61e_1000|hbdb9355_0|h76de61e_1000|h76de61e_0|he376013_2|h16faf7d_4|h16faf7d_0|h709d2b2_0|he6690cf_4|h9bf37e3_5|h9bf37e3_6|h8ef9fac_0|hf45b732_0|hf45b732_0|hf45b732_0|h97da3c1_1|hf45b732_1|hf45b732_0|hf45b732_2|h8ef9fac_1|h8ef9fac_0|h8ef9fac_0|h9bf37e3_8|he6690cf_1|he6690cf_0|he6690cf_0|hc0b9707_0|hc0b9707_1|h16faf7d_0|hc0b9707_1|h16faf7d_0|hc0b9707_5|hbdb9355_0|h76de61e_1002|hbdb9355_2|hb8e4fae_0|hb8e4fae_2|h051b688_0|h051b688_0|h051b688_0|h051b688_0|h051b688_0|h051b688_0|h051b688_1000|h051b688_0|h051b688_0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libcurl[version='>=7.62.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.76.1,<8.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libcurl[version='>=7.60.0,<8.0a0|>=7.61.0,<8.0a0|>=7.62.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.76.1,<8.0a0|>=7.78.0,<8.0a0|>=7.77.0,<8.0a0|>=7.71.0,<8.0a0|>=7.69.1,<8.0a0|>=7.67.0,<8.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libcurl[version='>=7.60.0,<8.0a0|>=7.61.0,<8.0a0|>=7.62.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.76.1,<8.0a0|>=7.78.0,<8.0a0|>=7.77.0,<8.0a0|>=7.71.0,<8.0a0|>=7.69.1,<8.0a0|>=7.67.0,<8.0a0']

Package libzlib conflicts for:
spades=3.15.2 -> python -> libzlib[version='1.2.11|1.2.11|>=1.2.11,<1.3.0a0',build='h9173be1_1012|h9173be1_1013']
kaptive=0.7.3 -> python[version='>=3'] -> libzlib[version='>=1.2.11,<1.3.0a0']
abricate=1.0.1 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
quast=5.0.2 -> python[version='>=3.7,<3.8.0a0'] -> libzlib[version='1.2.11|1.2.11|>=1.2.11,<1.3.0a0',build='h9173be1_1012|h9173be1_1013']
trimmomatic=0.39 -> python -> libzlib[version='>=1.2.11,<1.3.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> libzlib[version='1.2.11|1.2.11|>=1.2.11,<1.3.0a0',build='h9173be1_1012|h9173be1_1013']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0']
python=3.6.11 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
blast=2.10.1 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
sickle-trim=1.33 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
megahit=1.2.9 -> python -> libzlib[version='1.2.11|1.2.11|>=1.2.11,<1.3.0a0',build='h9173be1_1012|h9173be1_1013']
rdptools=2.0.3 -> python -> libzlib[version='>=1.2.11,<1.3.0a0']
sistr_cmd=1.1.1 -> python -> libzlib[version='>=1.2.11,<1.3.0a0']
r-base=3.6.3 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
tabulate=0.8.7 -> python -> libzlib[version='>=1.2.11,<1.3.0a0']
cgecore=1.5.6 -> python -> libzlib[version='>=1.2.11,<1.3.0a0']
mlst=2.19.0 -> zlib -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
git=2.28.0 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']

Package perl-bio-tools-run-alignment-clustalw conflicts for:
roary=3.13.0 -> perl-bioperl[version='>=1.7.2'] -> perl-bio-tools-run-alignment-clustalw
abricate=1.0.1 -> perl-bioperl[version='>=1.7'] -> perl-bio-tools-run-alignment-clustalw
mlst=2.19.0 -> perl-bioperl[version='>=1.7.2'] -> perl-bio-tools-run-alignment-clustalw
prokka=1.14.6 -> perl-bioperl[version='>=1.7.2'] -> perl-bio-tools-run-alignment-clustalw

Package glib conflicts for:
imagemagick=7.0.10_28 -> glib[version='>=2.58.3,<3.0a0']
r-base=3.6.3 -> cairo[version='>=1.16.0,<1.17.0a0'] -> glib[version='>=2.56.1,<2.57.0a0|>=2.56.1,<3.0a0|>=2.58.2,<2.59.0a0|>=2.58.3,<3.0a0|>=2.67.4,<3.0a0|>=2.63.1,<3.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> glib[version='>=2.56.1,<2.57.0a0|>=2.56.1,<3.0a0|>=2.63.1,<3.0a0']

Package r-stringi conflicts for:
r-stringi=1.4.6
r-rmarkdown=2.1 -> r-stringr[version='>=1.2.0'] -> r-stringi[version='>=0.4.1|>=1.1.6|>=1.1.7']
r-essentials=3.6 -> r-stringr[version='>=1.3.1'] -> r-stringi[version='>=1.1.6|>=1.1.7']
r-plotly=4.9.0 -> r-tidyr -> r-stringi

Package r-base conflicts for:
r-rmarkdown=2.1 -> r-base[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.5.1,<3.5.2.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0']
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-base[version='3.1.2|3.1.3|3.2.0|3.2.0.|3.2.1.|3.2.2.|3.3.2.|3.4.1.|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.5.0,<3.5.1.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0|3.3.1.|3.4.1|3.3.2|3.4.2.|3.3.1|3.2.2|3.2.1']
r-biocmanager=1.30.10 -> r-base[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0']
r-dt=0.5 -> r-crosstalk -> r-base[version='3.2.0.|3.2.1.|3.2.2.|3.3.2.|3.4.1.|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.0,<3.5.1.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0|3.3.1.']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0|>=3.6,<3.7.0a0']
r-base=3.6.3
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0']
r-rmarkdown=2.1 -> r-base64enc -> r-base[version='3.1.3.|3.2.0.|3.2.1.|3.2.2.|3.3.2.|3.4.1.|>=3.4.1,<3.4.2.0a0|>=3.5.1,<3.5.2.0a0|>=4.1,<4.2.0a0|>=3.5.0,<3.5.1.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0|3.3.1.']
r-plotly=4.9.0 -> r-base64enc -> r-base[version='3.1.3.|3.2.0.|3.2.1.|3.2.2.|3.3.2.|3.4.1.|>=3.4.1,<3.4.2.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.0,<3.5.1.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0|3.3.1.*']

Package libcxx conflicts for:
quast=5.0.2 -> blast -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=4.0.1|>=9.0.0']
abricate=1.0.1 -> blast[version='>=2.7'] -> libcxx[version='>=11.1.0|>=9.0.1|>=4.0.1']
blast=2.10.1 -> pcre[version='>=8.44,<9.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.1.0']
kraken2=2.0.9beta -> blast -> libcxx[version='>=11.1.0|>=9.0.1']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> libcxx[version='>=11.1.0|>=9.0.1|>=4.0.1']
blast=2.10.1 -> libcxx[version='>=9.0.1']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=4.0.1|>=9.0.1|>=9.0.0']
python=3.6.11 -> libcxx[version='>=10.0.1|>=11.0.0']
r-stringi=1.4.6 -> libcxx[version='>=10.0.0|>=9.0.1']
kaptive=0.7.3 -> biopython[version='<1.78'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=4.0.1|>=9.0.1|>=9.0.0']
spades=3.15.2 -> python -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.0|>=4.0.1']
rdptools=2.0.3 -> python -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1']
trimmomatic=0.39 -> openjdk -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1']
kraken2=2.0.9beta -> libcxx[version='>=4.0|>=4.0.1']
megahit=1.2.9 -> libcxx[version='>=4.0.1']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1|>=11.0.1']
barrnap=0.9 -> bedtools -> libcxx[version='>=11.1.0|>=9.0.1|>=4.0.1']
imagemagick=7.0.10_28 -> ghostscript -> libcxx[version='>=10.0.0|>=11.0.1|>=11.1.0|>=4.0.1|>=9.0.1|>=9.0.0']
imagemagick=7.0.10_28 -> libcxx[version='>=10.0.1|>=11.0.0']
r-stringi=1.4.6 -> icu[version='>=67.1,<68.0a0'] -> libcxx[version='>=10.0.1|>=11.1.0|>=11.0.0|>=9.0.0|>=4.0.1|>=11.0.1']
r-base=3.6.3 -> clangxx_osx-64[version='>=11'] -> libcxx[version='>=11.0.1|>=12.0.1|>=12.0.0|>=4.0.1|>=9.0.0']
roary=3.13.0 -> bedtools -> libcxx[version='>=11.1.0|>=9.0.1|>=4.0.1']
biopython=1.77 -> numpy -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=4.0.1|>=9.0.1|>=9.0.0']
mauve=2.4.0 -> openjdk -> libcxx[version='>=11.1.0']
cgecore=1.5.6 -> biopython -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=4.0.1|>=11.1.0|>=9.0.1|>=9.0.0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.1.0|>=4.0.1|>=9.0.1|>=9.0.0|>=11.0.1|>=11.0.0']
python=3.6.11 -> libffi[version='>=3.3,<3.4.0a0'] -> libcxx[version='>=10.0.0|>=4.0.1|>=9.0.1']
megahit=1.2.9 -> python -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=9.0.0']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> libcxx[version='>=11.1.0|>=9.0.1|>=4.0.1']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1|>=11.0.1']
git=2.28.0 -> expat[version='>=2.2.9,<3.0.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.1|>=11.1.0|>=9.0.1']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1|>=11.0.1']
spades=3.15.2 -> libcxx[version='>=9.0.1']
tabulate=0.8.7 -> python -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1']
r-base=3.6.3 -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=9.0.1']
sistr_cmd=1.1.1 -> blast -> libcxx[version='>=10.0.0|>=11.1.0|>=9.0.1|>=4.0.1|>=9.0.0|>=11.0.0|>=10.0.1|>=11.0.1']

Package curl conflicts for:
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> curl
r-base=3.6.3 -> curl
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> curl
quast=5.0.2 -> blast -> curl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']
sistr_cmd=1.1.1 -> blast -> curl[version='7.55.*|>=7.55.1,<8.0a0|>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']
git=2.28.0 -> curl[version='>=7.71.1,<8.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> curl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']
abricate=1.0.1 -> blast[version='>=2.7'] -> curl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']
kraken2=2.0.9beta -> blast -> curl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> curl
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> curl
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> curl
barrnap=0.9 -> bedtools -> curl[version='>=7.64.1,<8.0a0']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> curl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']
blast=2.10.1 -> curl[version='>=7.71.1,<8.0a0']
roary=3.13.0 -> bedtools -> curl[version='>=7.64.1,<8.0a0|>=7.77.0,<8.0a0|>=7.75.0,<8.0a0|>=7.71.1,<8.0a0|>=7.69.1,<8.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> curl
prokka=1.14.6 -> blast[version='>=2.7.1'] -> curl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0']

Package gmp conflicts for:
sistr_cmd=1.1.1 -> blast -> gmp[version='>=6.1.2,<7.0a0']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> gmp[version='>=6.1.2,<7.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> gmp[version='>=6.1.2,<7.0a0']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> gmp[version='>=6.1.2,<7.0a0']
kraken2=2.0.9beta -> blast -> gmp[version='>=6.1.2,<7.0a0']
fasttree=2.1.10 -> libgcc -> gmp[version='>=4.2']
quast=5.0.2 -> blast -> gmp[version='>=6.1.2,<7.0a0']
roary=3.13.0 -> blast -> gmp[version='>=6.1.2,<7.0a0']
abricate=1.0.1 -> blast[version='>=2.7'] -> gmp[version='>=6.1.2,<7.0a0']

Package biopython conflicts for:
kaptive=0.7.3 -> biopython[version='<1.78']
cgecore=1.5.6 -> biopython
biopython=1.77

Package tk conflicts for:
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
spades=3.15.2 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0']
git=2.28.0 -> tk[version='>=8.6.10,<8.7.0a0']
megahit=1.2.9 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
rdptools=2.0.3 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
kaptive=0.7.3 -> python[version='>=3'] -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
quast=5.0.2 -> python[version='>=3.7,<3.8.0a0'] -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
trimmomatic=0.39 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0']
r-base=3.6.3 -> tk[version='>=8.6.10,<8.7.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
python=3.6.11 -> tk[version='>=8.6.10,<8.7.0a0']
sistr_cmd=1.1.1 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
r-base=3.6.3 -> bwidget -> tk[version='>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
tabulate=0.8.7 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
cgecore=1.5.6 -> python -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']

Package blast conflicts for:
quast=5.0.2 -> blast
prokka=1.14.6 -> blast[version='>=2.7.1']
kraken2=2.0.9beta -> blast
mlst=2.19.0 -> blast[version='>=2.9.0']
sistr_cmd=1.1.1 -> blast
blast=2.10.1
kaptive=0.7.3 -> blast[version='>=2.3.0']
abricate=1.0.1 -> blast[version='>=2.7']
roary=3.13.0 -> blast

Package r conflicts for:
r-essentials=3.6 -> r-magrittr[version='>=1.5'] -> r[version='3.1.2|3.1.3|3.2.0|3.2.0.|3.2.1.|3.2.2.|3.3.1|3.2.2|3.2.1']
r-dt=0.5 -> r-magrittr -> r[version='3.2.0.|3.2.1.|3.2.2.']
r-plotly=4.9.0 -> r-base64enc -> r[version='3.1.3.|3.2.0.|3.2.1.|3.2.2.|3.3.1.']
r-rmarkdown=2.1 -> r-base64enc -> r[version='3.1.3.|3.2.0.|3.2.1.|3.2.2.*']

Package perl-scalar-list-utils conflicts for:
mlst=2.19.0 -> perl-moo -> perl-scalar-list-utils
roary=3.13.0 -> perl-moose -> perl-scalar-list-utils[version='>=1.45']

Package openjdk conflicts for:
rdptools=2.0.3 -> openjdk=8.0
mauve=2.4.0 -> openjdk=8.0.192
quast=5.0.2 -> openjdk[version='>=8']
prokka=1.14.6 -> minced[version='>=0.3'] -> openjdk[version='11.*|>=8']
trimmomatic=0.39 -> openjdk

Package r-dplyr conflicts for:
r-essentials=3.6 -> r-dplyr[version='>=0.7.6|>=0.7.8']
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-dplyr[version='>=0.7.0|>=0.8.2|>=1.0.5|>=0.8.3|>=0.7.4']

Package parallel conflicts for:
parallel=20200722
roary=3.13.0 -> parallel[version='>=20180522']
prokka=1.14.6 -> parallel[version='>=20180522']

Package pypy3.6 conflicts for:
biopython=1.77 -> numpy -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.*|>=7.3.2|>=7.3.3']
biopython=1.77 -> pypy3.6[version='>=7.3.1']

Package mmtf-python conflicts for:
cgecore=1.5.6 -> biopython -> mmtf-python
kaptive=0.7.3 -> biopython[version='<1.78'] -> mmtf-python

Package liblapack conflicts for:
r-base=3.6.3 -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
biopython=1.77 -> numpy -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
kaptive=0.7.3 -> numpy -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-dt=0.5 -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> liblapack[version='>=3.8.0,<4.0.0a0|>=3.8.0,<4.0a0']

Package bzip2 conflicts for:
imagemagick=7.0.10_28 -> bzip2[version='>=1.0.8,<2.0a0']
barrnap=0.9 -> bedtools -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
r-base=3.6.3 -> bzip2[version='>=1.0.8,<2.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
tabulate=0.8.7 -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
rdptools=2.0.3 -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
roary=3.13.0 -> bedtools -> bzip2[version='1.0.|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
cgecore=1.5.6 -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> bzip2[version='1.0.|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
trimmomatic=0.39 -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
spades=3.15.2 -> bzip2[version='>=1.0.8,<2.0a0']
kraken2=2.0.9beta -> blast -> bzip2[version='1.0.|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
megahit=1.2.9 -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
quast=5.0.2 -> blast -> bzip2[version='1.0.|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
blast=2.10.1 -> bzip2[version='>=1.0.8,<2.0a0']
spades=3.15.2 -> python -> bzip2[version='>=1.0.6,<2.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
abricate=1.0.1 -> blast[version='>=2.7'] -> bzip2[version='1.0.|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> bzip2[version='1.0.|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
sistr_cmd=1.1.1 -> blast -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']

Package mafft conflicts for:
roary=3.13.0 -> mafft
sistr_cmd=1.1.1 -> mafft

Package jpeg conflicts for:
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a|>=9d,<10a']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a|>=9d,<10a']
imagemagick=7.0.10_28 -> jpeg[version='>=9d,<10a']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a|>=9d,<10a']
r-base=3.6.3 -> jpeg[version='>=9c,<10a|>=9d,<10a']
r-base=3.6.3 -> libtiff[version='>=4.2.0,<5.0a0'] -> jpeg[version='>=9b,<10a']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a|>=9d,<10a']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a|>=9d,<10a']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> jpeg[version='>=9b,<10a|>=9c,<10a|>=9d,<10a']

Package tzdata conflicts for:
cgecore=1.5.6 -> python -> tzdata
trimmomatic=0.39 -> python -> tzdata
megahit=1.2.9 -> python -> tzdata
kaptive=0.7.3 -> python[version='>=3'] -> tzdata
rdptools=2.0.3 -> python -> tzdata
sistr_cmd=1.1.1 -> python -> tzdata
biopython=1.77 -> python[version='>=3.9,<3.10.0a0'] -> tzdata
tabulate=0.8.7 -> python -> tzdata
spades=3.15.2 -> python -> tzdata

Package pypy3.7 conflicts for:
quast=5.0.2 -> matplotlib-base -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|>=7.3.3|>=7.3.4|>=7.3.5']
tabulate=0.8.7 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.']
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|>=7.3.3|>=7.3.4|>=7.3.5']
r-essentials=3.6 -> notebook[version='>=5.7.2'] -> pypy3.7[version='>=7.3.3']
biopython=1.77 -> numpy -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|>=7.3.3|>=7.3.4|>=7.3.5']
spades=3.15.2 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.']
trimmomatic=0.39 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.']
megahit=1.2.9 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.']
kaptive=0.7.3 -> numpy -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|>=7.3.3|>=7.3.4|>=7.3.5']
cgecore=1.5.6 -> biopython -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|>=7.3.3|>=7.3.4']
rdptools=2.0.3 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.']

Package libssh2 conflicts for:
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.9.0,<2.0a0|>=1.8.2,<2.0a0|>=1.8.0,<2.0a0']
r-base=3.6.3 -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.9.0,<2.0a0']
git=2.28.0 -> curl[version='>=7.71.1,<8.0a0'] -> libssh2[version='>=1.10.0,<2.0a0|>=1.9.0,<2.0a0']
blast=2.10.1 -> curl[version='>=7.71.1,<8.0a0'] -> libssh2[version='>=1.10.0,<2.0a0|>=1.9.0,<2.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.9.0,<2.0a0|>=1.8.2,<2.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.9.0,<2.0a0|>=1.8.2,<2.0a0|>=1.8.0,<2.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.8.0,<2.0a0|>=1.9.0,<2.0a0|>=1.8.2,<2.0a0']
r-base=3.6.3 -> curl -> libssh2[version='1.*|>=1.10.0,<2.0a0|>=1.8.2,<2.0a0|>=1.8.0,<2.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.8.2,<2.0a0|>=1.8.0,<2.0a0|>=1.9.0,<2.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libssh2[version='>=1.8.0,<2.0.0a0|>=1.9.0,<2.0a0|>=1.8.2,<2.0a0|>=1.8.0,<2.0a0']

Package r-tidyr conflicts for:
r-essentials=3.6 -> r-tidyr[version='>=0.8.1']
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-tidyr[version='>=0.6.0|>=0.8.0|>=1.1.3|>=1.0.0|>=0.7.2']

Package bedtools conflicts for:
barrnap=0.9 -> bedtools
prokka=1.14.6 -> barrnap[version='>=0.7'] -> bedtools
roary=3.13.0 -> bedtools

Package perl-try-tiny conflicts for:
roary=3.13.0 -> perl-moose -> perl-try-tiny
perl-try-tiny=0.30
bioconda::perl-try-tiny-retry=0.004 -> perl-try-tiny

Package openssl conflicts for:
blast=2.10.1 -> curl[version='>=7.71.1,<8.0a0'] -> openssl[version='>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0']
r-base=3.6.3 -> curl -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.0.2m,<1.0.3a|>=1.1.1k,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.1.1,<1.1.2.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=3.0.0,<4.0a0|>=1.1.1l,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0|>=1.1.1b,<1.1.2a']
rdptools=2.0.3 -> python -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
git=2.28.0 -> curl[version='>=7.71.1,<8.0a0'] -> openssl[version='>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a']
git=2.28.0 -> openssl[version='>=1.1.1g,<1.1.2a']
tabulate=0.8.7 -> python -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
spades=3.15.2 -> python -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
roary=3.13.0 -> blast -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a']
kraken2=2.0.9beta -> blast -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1k,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1,<1.1.2.0a0']
abricate=1.0.1 -> blast[version='>=2.7'] -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a']
cgecore=1.5.6 -> python -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
quast=5.0.2 -> blast -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1j,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1,<1.1.2.0a0|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
sistr_cmd=1.1.1 -> blast -> openssl[version='1.0.|1.0.2.|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1k,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1j,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
trimmomatic=0.39 -> python -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']
python=3.6.11 -> openssl[version='>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a']
megahit=1.2.9 -> python -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a|>=1.1.1,<1.1.2.0a0']

Package libcxxabi conflicts for:
kraken2=2.0.9beta -> libcxx[version='>=4.0'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='hcfea43d_1|4|0|3|2|1|hebd6815_0']
megahit=1.2.9 -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='hcfea43d_1|4|0|3|2|1|hebd6815_0']

Package xorg-libsm conflicts for:
imagemagick=7.0.10_28 -> xorg-libxt -> xorg-libsm=1.2
r-essentials=3.6 -> r-rmarkdown[version='>=1.10'] -> xorg-libsm=1.2

Package libdeflate conflicts for:
r-base=3.6.3 -> libtiff[version='>=4.2.0,<5.0a0'] -> libdeflate[version='>=1.7,<1.8.0a0']
imagemagick=7.0.10_28 -> libtiff[version='>=4.1.0,<5.0a0'] -> libdeflate[version='>=1.7,<1.8.0a0']
roary=3.13.0 -> bedtools -> libdeflate[version='>=1.0,<1.1.0a0']
barrnap=0.9 -> bedtools -> libdeflate[version='>=1.0,<1.1.0a0']

Package xorg-libxext conflicts for:
mauve=2.4.0 -> xorg-libxi -> xorg-libxext=1.3
r-essentials=3.6 -> r-rmarkdown[version='>=1.10'] -> xorg-libxext=1.3
imagemagick=7.0.10_28 -> xorg-libxext

Package gettext conflicts for:
imagemagick=7.0.10_28 -> libglib[version='>=2.66.4,<3.0a0'] -> gettext[version='>=0.19.8.1,<1.0a0|>=0.21.0,<1.0a0']
git=2.28.0 -> gettext[version='>=0.19.8.1,<1.0a0']
r-base=3.6.3 -> libglib[version='>=2.68.2,<3.0a0'] -> gettext[version='>=0.19.8.1,<1.0a0']

Package pcre conflicts for:
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.43,<9.0a0|>=8.44,<9.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.43,<9.0a0|>=8.42,<9.0a0|>=8.44,<9.0a0']
kraken2=2.0.9beta -> blast -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.42,<9.0a0|>=8.45,<9.0a0|>=8.44,<9.0a0|>=8.43,<9.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.43,<9.0a0|>=8.42,<9.0a0|>=8.44,<9.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.43,<9.0a0|>=8.44,<9.0a0|>=8.42,<9.0a0']
git=2.28.0 -> pcre[version='>=8.44,<9.0a0']
quast=5.0.2 -> blast -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
roary=3.13.0 -> blast -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
abricate=1.0.1 -> blast[version='>=2.7'] -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.43,<9.0a0|>=8.44,<9.0a0|>=8.42,<9.0a0']
r-base=3.6.3 -> libglib[version='>=2.68.2,<3.0a0'] -> pcre[version='>=8.45,<9.0a0']
r-base=3.6.3 -> pcre[version='>=8.44,<9.0a0']
sistr_cmd=1.1.1 -> blast -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
blast=2.10.1 -> pcre[version='>=8.44,<9.0a0']
mlst=2.19.0 -> blast[version='>=2.9.0'] -> pcre[version='>=8.41,<9.0a0|>=8.44,<9.0a0|>=8.45,<9.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> pcre[version='>=8.41,<9.0a0|>=8.43,<9.0a0|>=8.44,<9.0a0|>=8.42,<9.0a0']

Package libedit conflicts for:
r-base=3.6.3 -> krb5[version='>=1.19.1,<1.20.0a0'] -> libedit[version='>=3.1.20170329,<4.0a0|>=3.1.20191231,<3.2.0a0|>=3.1.20191231,<4.0a0|>=3.1.20210216,<3.2.0a0|>=3.1.20210216,<4.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20181209,<4.0a0']
python=3.6.11 -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20191231,<3.2.0a0']

Package setuptools conflicts for:
quast=5.0.2 -> joblib -> setuptools
python=3.6.11 -> pip -> setuptools

Package libffi conflicts for:
python=3.6.11 -> libffi[version='>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> libffi[version='>=3.2.1,<3.3.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0|>=3.4.2,<3.5.0a0|>=3.3,<3.4.0a0']
tabulate=0.8.7 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
spades=3.15.2 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
git=2.28.0 -> gettext[version='>=0.19.8.1,<1.0a0'] -> libffi[version='>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
cgecore=1.5.6 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
megahit=1.2.9 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
trimmomatic=0.39 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
kaptive=0.7.3 -> python[version='>=3'] -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
quast=5.0.2 -> python[version='>=3.7,<3.8.0a0'] -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
r-base=3.6.3 -> libglib[version='>=2.68.2,<3.0a0'] -> libffi[version='>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
sistr_cmd=1.1.1 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']
rdptools=2.0.3 -> python -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.4.2,<3.5.0a0|>=3.2.1,<3.3a0|>=3.2.1,<4.0a0']

Package ca-certificates conflicts for:
sistr_cmd=1.1.1 -> python -> ca-certificates
quast=5.0.2 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
tabulate=0.8.7 -> python -> ca-certificates
cgecore=1.5.6 -> python -> ca-certificates
git=2.28.0 -> openssl[version='>=1.1.1g,<1.1.2a'] -> ca-certificates
megahit=1.2.9 -> python -> ca-certificates
rdptools=2.0.3 -> python -> ca-certificates
python=3.6.11 -> openssl[version='>=1.1.1h,<1.1.2a'] -> ca-certificates
trimmomatic=0.39 -> python -> ca-certificates
spades=3.15.2 -> python -> ca-certificates

Package r-mime conflicts for:
r-plotly=4.9.0 -> r-httr -> r-mime
r-essentials=3.6 -> r-httr[version='>=1.3.1'] -> r-mime[version='>=0.3']
r-rmarkdown=2.1 -> r-mime

Package pcre2 conflicts for:
r-stringi=1.4.6 -> r-base[version='>=4.0,<4.1.0a0'] -> pcre2[version='>=10.34,<10.35.0a0|>=10.35,<10.36.0a0|>=10.36,<10.37.0a0|>=10.37,<10.38.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=4.0,<4.1.0a0'] -> pcre2[version='>=10.34,<10.35.0a0|>=10.35,<10.36.0a0|>=10.36,<10.37.0a0|>=10.37,<10.38.0a0']
r-rmarkdown=2.1 -> r-base[version='>=4.0,<4.1.0a0'] -> pcre2[version='>=10.34,<10.35.0a0|>=10.35,<10.36.0a0|>=10.36,<10.37.0a0|>=10.37,<10.38.0a0']

Package libxml2 conflicts for:
git=2.28.0 -> gettext[version='>=0.19.8.1,<1.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0|>=2.9.12,<2.10.0a0']
mauve=2.4.0 -> fontconfig -> libxml2[version='2.9.*|>=2.9.10,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0|>=2.9.7,<2.10.0a0|>=2.9.4,<2.10.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.12,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.12,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.12,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.12,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0']
imagemagick=7.0.10_28 -> fontconfig[version='>=2.13.1,<3.0a0'] -> libxml2[version='>=2.9.12,<2.10.0a0|>=2.9.8,<2.10.0a0|>=2.9.9,<2.10.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0|>=2.9.12,<2.10.0a0']
r-base=3.6.3 -> libxml2[version='>=2.9.10,<2.10.0a0|>=2.9.12,<2.10.0a0']
imagemagick=7.0.10_28 -> libxml2[version='>=2.9.10,<2.10.0a0']

Package ncurses conflicts for:
spades=3.15.2 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0']
quast=5.0.2 -> python[version='>=3.7,<3.8.0a0'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.2,<6.3.0a0']
cgecore=1.5.6 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
python=3.6.11 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='>=6.1,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0']
trimmomatic=0.39 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
megahit=1.2.9 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.2,<6.3.0a0']
kaptive=0.7.3 -> python[version='>=3'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
biopython=1.77 -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.2,<6.3.0a0']
r-base=3.6.3 -> ncurses[version='>=6.2,<6.3.0a0']
tabulate=0.8.7 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.2,<7.0a0|>=6.2,<6.3.0a0']
python=3.6.11 -> ncurses[version='>=6.2,<6.3.0a0']
sistr_cmd=1.1.1 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0']
r-base=3.6.3 -> readline[version='>=8.1,<9.0a0'] -> ncurses[version='>=6.1,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
rdptools=2.0.3 -> python -> ncurses[version='>=6.0,<7.0a0|>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']

Package numpy-base conflicts for:
biopython=1.77 -> numpy -> numpy-base[version='1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.17.2.|1.17.3.|1.17.4.|1.18.1.|1.18.5.|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|>=1.9.3,<2.0a0|1.17.0|1.17.0',build='py27h9797aa9_6|py37h9797aa9_6|py36h9797aa9_6|py37ha9ae307_6|py36ha9ae307_6|py37h9797aa9_7|py35ha9ae307_7|py36ha9ae307_7|py27ha9ae307_7|py36ha9ae307_7|py27h9797aa9_8|py36ha9ae307_8|py37ha9ae307_8|py37h9797aa9_8|py35h9797aa9_8|py35ha9ae307_8|py37he97cb71_9|py35he97cb71_9|py35h42e5f7b_10|py27h8a80b8c_10|py35h8a80b8c_10|py37h8a80b8c_10|py36h42e5f7b_10|py37ha711998_11|py27ha711998_11|py27h6575580_11|py36h6575580_11|py37ha711998_12|py36ha711998_12|py37h6575580_12|py38ha711998_13|py38ha711998_14|py38h6575580_14|py38h6575580_15|py36h479e554_1|py35h479e554_1|py35h7ef55bc_1|py27h9797aa9_0|py27ha9ae307_0|py36ha9ae307_0|py36h9797aa9_0|py35ha9ae307_0|py36h9797aa9_0|py27h9797aa9_0|py27ha9ae307_0|py35ha9ae307_0|py27h9797aa9_1|py36h9797aa9_1|py37h9797aa9_1|py37ha9ae307_1|py36ha9ae307_1|py36h9797aa9_2|py27h9797aa9_2|py37ha9ae307_2|py27h9797aa9_3|py36h9797aa9_3|py27ha9ae307_3|py37ha9ae307_3|py27ha9ae307_4|py27h9797aa9_4|py36ha9ae307_4|py36h9797aa9_4|py37ha9ae307_4|py35h9797aa9_4|py35ha711998_4|py35h8a80b8c_4|py37ha711998_4|py27ha711998_4|py36h8a80b8c_4|py27h8a80b8c_4|py38ha711998_4|py38h6575580_4|py37h6575580_5|py27he97cb71_0|py27h8a80b8c_0|py37he97cb71_0|py36he97cb71_0|py35h42e5f7b_0|py36h42e5f7b_0|py27h8a80b8c_0|py37h8a80b8c_0|py35h8a80b8c_0|py35ha711998_0|py27h8a80b8c_0|py35ha711998_0|py27ha711998_1|py37ha711998_1|py36ha711998_1|py37h8a80b8c_1|py37h8a80b8c_0|py27h8a80b8c_0|py37h8a80b8c_0|py37h6575580_0|py27h6575580_0|py36h6575580_0|py37h6575580_0|py27ha711998_1|py36ha711998_1|py27h6575580_1|py27h6575580_0|py37h6575580_0|py36ha711998_1|py27h6575580_1|py27ha711998_1|py37ha711998_1|py36h6575580_1|py27ha711998_0|py27h6575580_0|py37h6575580_0|py27h6575580_0|py37h6575580_0|py36h6575580_0|py37ha711998_0|py27ha711998_0|py27h6575580_0|py37h6575580_0|py36ha711998_0|py37h6575580_0|py38h6575580_0|py39h7ca7dfd_1|py38hd037223_3|py39h4850c68_3|py36h4850c68_3|py37hcfb5961_0|py36hcfb5961_0|py38hcfb5961_0|py36hcfb5961_0|py38hcfb5961_0|py37h68fea81_0|py39h3a452eb_0|py39he0bd621_0|py37hbbe2e76_0|py38he0bd621_0|py37he0bd621_0|py37hbbe2e76_0|py38hbbe2e76_0|py37he0bd621_0|py39he0bd621_0|py38he0bd621_0|py39hbbe2e76_0|py38hbbe2e76_0|py39hbbe2e76_0|py38h585ceec_0|py38h3a452eb_0|py37h585ceec_0|py37h3a452eb_0|py39h585ceec_0|py39h3a452eb_0|py39hde55871_0|py36h68fea81_0|py38h68fea81_0|py37hcfb5961_0|py37h68fea81_0|py38h68fea81_0|py36h68fea81_0|py37h4850c68_3|py38h4850c68_3|py37hd037223_3|py36hd037223_3|py39hd037223_3|py39hd037223_1|py27h6575580_0|py27ha711998_0|py38ha711998_0|py36h6575580_0|py37ha711998_0|py36h6575580_0|py36ha711998_0|py27h6575580_0|py27ha711998_0|py37ha711998_0|py36ha711998_0|py36h6575580_0|py37ha711998_0|py27ha711998_0|py36ha711998_0|py37h6575580_0|py37ha711998_0|py36h6575580_0|py36ha711998_0|py37h6575580_1|py37ha711998_0|py36h6575580_0|py27ha711998_0|py36ha711998_0|py36h6575580_1|py37ha711998_1|py37h6575580_1|py36h6575580_0|py27h6575580_0|py36ha711998_0|py37ha711998_0|py27ha711998_0|py37ha711998_0|py36ha711998_0|py27ha711998_0|py36h8a80b8c_0|py27h8a80b8c_0|py36h8a80b8c_0|py36ha711998_0|py27ha71199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kaptive=0.7.3 -> numpy -> numpy-base[version='1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.17.2.|1.17.3.|1.17.4.|1.18.1.|1.18.5.|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|>=1.9.3,<2.0a0|1.17.0|1.17.0',build='py27h9797aa9_6|py37h9797aa9_6|py36h9797aa9_6|py37ha9ae307_6|py36ha9ae307_6|py37h9797aa9_7|py35ha9ae307_7|py36ha9ae307_7|py27ha9ae307_7|py36ha9ae307_7|py27h9797aa9_8|py36ha9ae307_8|py37ha9ae307_8|py37h9797aa9_8|py35h9797aa9_8|py35ha9ae307_8|py37he97cb71_9|py35he97cb71_9|py35h42e5f7b_10|py27h8a80b8c_10|py35h8a80b8c_10|py37h8a80b8c_10|py36h42e5f7b_10|py37ha711998_11|py27ha711998_11|py27h6575580_11|py36h6575580_11|py37ha711998_12|py36ha711998_12|py37h6575580_12|py38ha711998_13|py38ha711998_14|py38h6575580_14|py38h6575580_15|py36h479e554_1|py35h479e554_1|py35h7ef55bc_1|py27h9797aa9_0|py27ha9ae307_0|py36ha9ae307_0|py36h9797aa9_0|py35ha9ae307_0|py36h9797aa9_0|py27h9797aa9_0|py27ha9ae307_0|py35ha9ae307_0|py27h9797aa9_1|py36h9797aa9_1|py37h9797aa9_1|py37ha9ae307_1|py36ha9ae307_1|py36h9797aa9_2|py27h9797aa9_2|py37ha9ae307_2|py27h9797aa9_3|py36h9797aa9_3|py27ha9ae307_3|py37ha9ae307_3|py27ha9ae307_4|py27h9797aa9_4|py36ha9ae307_4|py36h9797aa9_4|py37ha9ae307_4|py35h9797aa9_4|py35ha711998_4|py35h8a80b8c_4|py37ha711998_4|py27ha711998_4|py36h8a80b8c_4|py27h8a80b8c_4|py38ha711998_4|py38h6575580_4|py37h6575580_5|py27he97cb71_0|py27h8a80b8c_0|py37he97cb71_0|py36he97cb71_0|py35h42e5f7b_0|py36h42e5f7b_0|py27h8a80b8c_0|py37h8a80b8c_0|py35h8a80b8c_0|py35ha711998_0|py27h8a80b8c_0|py35ha711998_0|py27ha711998_1|py37ha711998_1|py36ha711998_1|py37h8a80b8c_1|py37h8a80b8c_0|py27h8a80b8c_0|py37h8a80b8c_0|py37h6575580_0|py27h6575580_0|py36h6575580_0|py37h6575580_0|py27ha711998_1|py36ha711998_1|py27h6575580_1|py27h6575580_0|py37h6575580_0|py36ha711998_1|py27h6575580_1|py27ha711998_1|py37ha711998_1|py36h6575580_1|py27ha711998_0|py27h6575580_0|py37h6575580_0|py27h6575580_0|py37h6575580_0|py36h6575580_0|py37ha711998_0|py27ha711998_0|py27h6575580_0|py37h6575580_0|py36ha711998_0|py37h6575580_0|py38h6575580_0|py39h7ca7dfd_1|py38hd037223_3|py39h4850c68_3|py36h4850c68_3|py37hcfb5961_0|py36hcfb5961_0|py38hcfb5961_0|py36hcfb5961_0|py38hcfb5961_0|py37h68fea81_0|py39h3a452eb_0|py39he0bd621_0|py37hbbe2e76_0|py38he0bd621_0|py37he0bd621_0|py37hbbe2e76_0|py38hbbe2e76_0|py37he0bd621_0|py39he0bd621_0|py38he0bd621_0|py39hbbe2e76_0|py38hbbe2e76_0|py39hbbe2e76_0|py38h585ceec_0|py38h3a452eb_0|py37h585ceec_0|py37h3a452eb_0|py39h585ceec_0|py39h3a452eb_0|py39hde55871_0|py36h68fea81_0|py38h68fea81_0|py37hcfb5961_0|py37h68fea81_0|py38h68fea81_0|py36h68fea81_0|py37h4850c68_3|py38h4850c68_3|py37hd037223_3|py36hd037223_3|py39hd037223_3|py39hd037223_1|py27h6575580_0|py27ha711998_0|py38ha711998_0|py36h6575580_0|py37ha711998_0|py36h6575580_0|py36ha711998_0|py27h6575580_0|py27ha711998_0|py37ha711998_0|py36ha711998_0|py36h6575580_0|py37ha711998_0|py27ha711998_0|py36ha711998_0|py37h6575580_0|py37ha711998_0|py36h6575580_0|py36ha711998_0|py37h6575580_1|py37ha711998_0|py36h6575580_0|py27ha711998_0|py36ha711998_0|py36h6575580_1|py37ha711998_1|py37h6575580_1|py36h6575580_0|py27h6575580_0|py36ha711998_0|py37ha711998_0|py27ha711998_0|py37ha711998_0|py36ha711998_0|py27ha711998_0|py36h8a80b8c_0|py27h8a80b8c_0|py36h8a80b8c_0|py36ha711998_0|py27ha71199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sistr_cmd=1.1.1 -> numpy[version='>=1.11.1'] -> 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Package r-purrr conflicts for:
r-essentials=3.6 -> r-purrr[version='>=0.2.5']
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-purrr[version='>=0.2.2|>=0.3.4|>=0.3.3|>=0.2.4']

Package r-later conflicts for:
r-plotly=4.9.0 -> r-promises -> r-later
r-essentials=3.6 -> r-shiny[version='>=1.2.0'] -> r-later[version='>=0.7.2|>=1.0.0']
r-dt=0.5 -> r-promises -> r-later

Package gnutls conflicts for:
mlst=2.19.0 -> blast[version='>=2.9.0'] -> gnutls[version='>=3.6.5,<3.7.0a0']
kaptive=0.7.3 -> blast[version='>=2.3.0'] -> gnutls[version='>=3.6.5,<3.7.0a0']
quast=5.0.2 -> blast -> gnutls[version='>=3.6.5,<3.7.0a0']
roary=3.13.0 -> blast -> gnutls[version='>=3.6.5,<3.7.0a0']
kraken2=2.0.9beta -> blast -> gnutls[version='>=3.6.5,<3.7.0a0']
prokka=1.14.6 -> blast[version='>=2.7.1'] -> gnutls[version='>=3.6.5,<3.7.0a0']
abricate=1.0.1 -> blast[version='>=2.7'] -> gnutls[version='>=3.6.5,<3.7.0a0']
sistr_cmd=1.1.1 -> blast -> gnutls[version='>=3.6.5,<3.7.0a0']

Package r-jsonlite conflicts for:
r-essentials=3.6 -> r-httr[version='>=1.3.1'] -> r-jsonlite[version='>=0.9.16|>=0.9.6|>=1.7.2|>=1.6']
r-essentials=3.6 -> r-jsonlite[version='>=1.5']

Package fontconfig conflicts for:
r-base=3.6.3 -> cairo[version='>=1.16.0,<1.17.0a0'] -> fontconfig[version='>=2.13.0,<3.0a0|>=2.13.1,<3.0a0']
imagemagick=7.0.10_28 -> fontconfig[version='>=2.13.1,<3.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> fontconfig[version='>=2.13.0,<3.0a0']
mauve=2.4.0 -> fontconfig[version='>=2.13.1,<3.0a0']

Package gsl conflicts for:
r-stringi=1.4.6 -> r-base[version='>=3.6,<3.7.0a0'] -> gsl[version='>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0|>=2.7,<2.8.0a0']
r-essentials=3.6 -> r-base[version='>=3.6,<3.7.0a0'] -> gsl[version='>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0']
r-dt=0.5 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> gsl[version='>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0']
r-rmarkdown=2.1 -> r-base[version='>=3.6,<3.7.0a0'] -> gsl[version='>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0|>=2.7,<2.8.0a0']
r-biocmanager=1.30.10 -> r-base[version='>=3.6,<3.7.0a0'] -> gsl[version='>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0|>=2.7,<2.8.0a0']
r-plotly=4.9.0 -> r-base[version='>=3.5,<3.6.0a0'] -> gsl[version='>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0']
r-base=3.6.3 -> gsl[version='>=2.6,<2.7.0a0']
sistr_cmd=1.1.1 -> mash -> gsl[version='1.16.|2.2.|>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0']

Package libgcc conflicts for:
quast=5.0.2 -> minimap2[version='>=2.10'] -> libgcc
prokka=1.14.6 -> barrnap[version='>=0.7'] -> libgcc
barrnap=0.9 -> bedtools -> libgcc
r-dt=0.5 -> r-htmltools[version='>=0.3.6'] -> libgcc
fasttree=2.1.10 -> libgcc
r-essentials=3.6 -> r-haven[version='>=1.1.2'] -> libgcc
r-rmarkdown=2.1 -> r-base64enc -> libgcc
r-plotly=4.9.0 -> r-base64enc -> libgcc
sistr_cmd=1.1.1 -> mash -> libgcc
abricate=1.0.1 -> perl-lwp-simple -> libgcc
roary=3.13.0 -> bedtools -> libgcc

Package perl-xml-simple conflicts for:
blast=2.10.1 -> entrez-direct -> perl-xml-simple
prokka=1.14.6 -> perl-xml-simple

Package expat conflicts for:
biopython=1.77 -> pypy3.6[version='>=7.3.1'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.2.9,<3.0.0a0']
imagemagick=7.0.10_28 -> graphviz[version='>=2.40.1,<3.0a0'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.5,<3.0a0']
git=2.28.0 -> expat[version='>=2.2.9,<3.0.0a0']

Package r-crosstalk conflicts for:
r-plotly=4.9.0 -> r-crosstalk
r-dt=0.5 -> r-crosstalk

Package perl-http-date conflicts for:
blast=2.10.1 -> entrez-direct -> perl-http-date
abricate=1.0.1 -> perl-lwp-simple -> perl-http-date

Package zstd conflicts for:
r-base=3.6.3 -> libtiff[version='>=4.2.0,<5.0a0'] -> zstd[version='>=1.3.7,<1.3.8.0a0|>=1.4.4,<1.5.0a0|>=1.4|>=1.4.3,<1.5.0.0a0|>=1.4.4,<1.5.0.0a0|>=1.4.5,<1.5.0a0|>=1.4.9,<1.5.0a0|>=1.5.0,<1.6.0a0|>=1.4.4,<1.4.5.0a0']
kraken2=2.0.9beta -> rsync -> zstd[version='>=1.4.5,<1.5.0a0|>=1.4.8,<1.5.0a0|>=1.5.0,<1.6.0a0']
imagemagick=7.0.10_28 -> libtiff[version='>=4.1.0,<5.0a0'] -> zstd[version='>=1.3.7,<1.3.8.0a0|>=1.4.4,<1.5.0a0|>=1.4|>=1.4.3,<1.5.0.0a0|>=1.4.4,<1.5.0.0a0|>=1.4.5,<1.5.0a0|>=1.4.9,<1.5.0a0|>=1.5.0,<1.6.0a0|>=1.4.4,<1.4.5.0a0']

Package openblas conflicts for:
biopython=1.77 -> numpy -> openblas[version='0.2.18.|0.2.18|0.2.18.|0.2.19|0.2.19.|0.2.20|0.2.20.|>=0.2.20,<0.2.21.0a0|>=0.3.3,<0.3.4.0a0|>=0.2.15']
r-base=3.6.3 -> libblas[version='>=3.8.0,<4.0a0'] -> openblas[version='0.3.5.|>=0.3.6,<0.3.7.0a0']
sistr_cmd=1.1.1 -> mash -> openblas[version='0.2.18.|0.2.18|0.2.18.|0.2.19|0.2.19.|0.2.20|0.2.20.|>=0.2.20,<0.2.21.0a0|>=0.3.3,<0.3.4.0a0|>=0.2.15']
kaptive=0.7.3 -> numpy -> openblas[version='0.2.18.|0.2.18|0.2.18.|0.2.19|0.2.19.|0.2.20|0.2.20.*|>=0.2.20,<0.2.21.0a0|>=0.3.3,<0.3.4.0a0|>=0.2.15']

Package numpy conflicts for:
kaptive=0.7.3 -> biopython[version='<1.78'] -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.8|>=1.11.3,<2.0a0|>=1.9.3,<2.0a0']
sistr_cmd=1.1.1 -> pandas[version='>=0.18.1,<=1.0.5'] -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.|>=1.12.1,<2.0a0|>=1.14.6,<2.0a0|>=1.18.5,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.9.3,<2.0a0|>=1.9.|>=1.9|>=1.8|>=1.7|>=1.13.3,<2.0a0|>=1.11.3,<2.0a0|>=1.9.3,<1.10.0a0|>=1.19.5,<2.0a0|>=1.16.6,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.15.1,<2.0a0|>=1.15.4,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0']
biopython=1.77 -> numpy
quast=5.0.2 -> matplotlib-base -> numpy[version='1.10.|1.11.|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.15.4,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.9.3,<2.0a0']
cgecore=1.5.6 -> biopython -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.8|>=1.11.3,<2.0a0|>=1.9.3,<2.0a0']
kaptive=0.7.3 -> numpy
sistr_cmd=1.1.1 -> numpy[version='>=1.11.1']

Package r-reshape2 conflicts for:
r-essentials=3.6 -> r-reshape2[version='>=1.4.3']
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-reshape2

Package r-tibble conflicts for:
r-essentials=3.6 -> r-tibble[version='>=1.4.2']
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-tibble[version='>=1.1|>=1.3.1|>=2.0.0|>=2.1.3|>=2.1.1|>=3.1.0|>=1.3.4']

Package python-dateutil conflicts for:
sistr_cmd=1.1.1 -> python-dateutil
sistr_cmd=1.1.1 -> pandas[version='>=0.18.1,<=1.0.5'] -> python-dateutil[version='>=2.5.*|>=2.6.1|>=2.7.3']

Package perl-libwww-perl conflicts for:
abricate=1.0.1 -> perl-lwp-simple -> perl-libwww-perl
roary=3.13.0 -> perl-digest-md5-file -> perl-libwww-perl

Package perl-pathtools conflicts for:
blast=2.10.1 -> perl-archive-tar -> perl-pathtools
roary=3.13.0 -> perl-file-find-rule -> perl-pathtools

Package perl-app-cpanminus conflicts for:
abricate=1.0.1 -> perl-list-moreutils -> perl-app-cpanminus
roary=3.13.0 -> perl-file-find-rule -> perl-app-cpanminus
blast=2.10.1 -> perl-list-moreutils -> perl-app-cpanminus
mlst=2.19.0 -> perl-list-moreutils -> perl-app-cpanminus

Package r-ggplot2 conflicts for:
r-essentials=3.6 -> r-ggplot2[version='>=3.0.0|>=3.1.0']
r-essentials=3.6 -> r-caret[version='>=6.0_80'] -> r-ggplot2[version='>=2.2.1|>=3.2.1|>=3.3.3']

Package barrnap conflicts for:
barrnap=0.9
prokka=1.14.6 -> barrnap[version='>=0.7']

Package r-stringr conflicts for:
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-stringr[version='>=1.2.0|>=1.4.0']
r-essentials=3.6 -> r-stringr[version='>=1.3.1']

Package r-magrittr conflicts for:
r-essentials=3.6 -> r-forcats[version='>=0.3.0'] -> r-magrittr[version='>=2.0.1']
r-essentials=3.6 -> r-magrittr[version='>=1.5']

Package tornado conflicts for:
r-essentials=3.6 -> notebook[version='>=5.7.2'] -> tornado[version='>=4|>=4,<6|>=4.1,<7|>=5.0,<7|>=5.0|>=6.1']
quast=5.0.2 -> matplotlib-base -> tornado

Package any2fasta conflicts for:
mlst=2.19.0 -> any2fasta
abricate=1.0.1 -> any2fasta

Package r-pkgconfig conflicts for:
r-plotly=4.9.0 -> r-dplyr -> r-pkgconfig[version='>=2.0.1|>=2.0.2']
r-essentials=3.6 -> r-dplyr[version='>=0.7.8'] -> r-pkgconfig[version='>=2.0.1|>=2.0.2']

Package r-plyr conflicts for:
r-essentials=3.6 -> r-broom[version='>=0.5.0'] -> r-plyr[version='>=1.7.1|>=1.8.1']
r-essentials=3.6 -> r-plyr[version='>=1.8.4']

Package fasttree conflicts for:
roary=3.13.0 -> fasttree
fasttree=2.1.10

Package r-rmarkdown conflicts for:
r-rmarkdown=2.1
r-essentials=3.6 -> r-rmarkdown[version='>=1.10']

Package xorg-libx11 conflicts for:
imagemagick=7.0.10_28 -> xorg-libx11
imagemagick=7.0.10_28 -> xorg-libxext -> xorg-libx11[version='1.6.*|>=1.7.0,<2.0a0']

Package xorg-renderproto conflicts for:
imagemagick=7.0.10_28 -> xorg-libxrender -> xorg-renderproto
mauve=2.4.0 -> xorg-libxrender -> xorg-renderproto

Package r-httr conflicts for:
r-essentials=3.6 -> r-rvest[version='>=0.3.2'] -> r-httr[version='>=0.5|>=1.4.2|>=1.4.1']
r-essentials=3.6 -> r-httr[version='>=1.3.1']

Package pytz conflicts for:
quast=5.0.2 -> matplotlib-base -> pytz
sistr_cmd=1.1.1 -> pandas[version='>=0.18.1,<=1.0.5'] -> pytz[version='>=2017.2|>=2017.3']

(base) vincenzopennone@MacBook-Pro-di-vincenzo ~ %

[nmquijada]

Hi Vincenzo,

Yep, there seems to be "some" conflicts... Definitely, burning your mac down would be a good solution, but let's try to find something less dramatic hahaha
Don't worry, you didn't do anything wrong. Conflicts between packages with conda sometimes occur and I never tested the installation on a MacOS BigSur. We are going to install tormes now without using any yml file, just by installing the required dependencies without specifying any version at this point.

First, to be sure, let's make the clean up and the configuration of channels (make sure you don't have any environment activated, just the "base" one from conda):

conda update conda
conda config --add channels anaconda
conda config --add channels r
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda env remove -n tormes-1.3.0 #in case you have it installed
conda clean --all

Do you have any old tormes environment installed? You can inspect so by doing conda env list. If so, please remove it and do the conda clean --all step afterwards.

Then create and environment that will host tormes, and let's install only that package:

conda create -n tormes-1.3.0 python=3.6 r-base=3.6 r-essentials
conda activate tormes-1.3.0
conda install -c nmquijada tormes=1.3.0

Now, let's try to install all the required dependencies one by one, and let's leave the conda configuration of your system to decide the compatible versions. This process can take a while... Usually, you should install all/most dependencies at once, but I would like to see what is failing for you. So:

for i in abricate ant biopython cgecore fasttree git imagemagick kaptive kraken2 mauve mauvealigner megahit mlst parallel perl-data-dumper perl-try-tiny bioconda::perl-try-tiny-retry prinseq prokka quast r-biocmanager r-dt r-plotly r-rmarkdown r-stringi rdptools roary sickle-trim sistr_cmd spades tabulate trimmomatic; do conda install -y ${i}; done

As dependencies will be installed one after the other in this "for" loop, it would be hard to check errors (if occur). Therefore, I would like to ask you to send me the file containing the configuration of your new tormes environment ("tormes-package-list.txt"):

conda list --show-channel-urls > tormes-package-list.txt

With this file I might be able to see which versions of the packages installed in your system and if some of them failed (if any).

Let me know!

Narciso

[vincenzopennone]

Hi Narciso,

Thanks a lot for your answer again!
So, I followed your guidelines on cleaning and configuration of Conda channels, checked that I didn't have any old tormes env, created and activated the tormes-1.3.0 env, but when I run the conda install -c nmquijada tormes=1.3.0 i get this:

(tormes-1.3.0) vincenzopennone@MacBook-Pro-di-vincenzo ~ % conda install -c nmquijada tormes=1.3.0

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• tormes=1.3.0

Current channels:

• https://conda.anaconda.org/nmquijada/osx-64
• https://conda.anaconda.org/nmquijada/noarch
• https://conda.anaconda.org/conda-forge/osx-64
• https://conda.anaconda.org/conda-forge/noarch
• https://conda.anaconda.org/bioconda/osx-64
• https://conda.anaconda.org/bioconda/noarch
• https://repo.anaconda.com/pkgs/main/osx-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/osx-64
• https://repo.anaconda.com/pkgs/r/noarch
• https://conda.anaconda.org/r/osx-64
• https://conda.anaconda.org/r/noarch
• https://conda.anaconda.org/anaconda/osx-64
• https://conda.anaconda.org/anaconda/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(tormes-1.3.0) vincenzopennone@MacBook-Pro-di-vincenzo ~ %

So, I guess the issue is here, or at least... it starts from here!

Regards,

Vincenzo

[nmquijada]

Hi Vincenzo,

OK I see. Your conda is looking in "osx-64" and "noarch" which is platform dependent and therefore cannot find tormes, as it's a linux-64 build.

I am sorry that this is taking long, but we'll get it!
We will try now to install tormes locally, without using any of the conda channels, by downloading the package directly from the source location. So you have your tormes-1.3.0 environment created with python v3.6 an R v3.6, right?. Then let's try to install tormes this way:

conda activate tormes-1.3.0
wget https://anaconda.org/nmquijada/tormes/1.3.0/download/linux-64/tormes-1.3.0-py36_0.tar.bz2
conda install -c local tormes-1.3.0-py36_0.tar.bz2

If it worked, try to install the rest of dependencies:

for i in abricate ant biopython cgecore fasttree git imagemagick kaptive kraken2 mauve mauvealigner megahit mlst parallel perl-data-dumper perl-try-tiny bioconda::perl-try-tiny-retry prinseq prokka quast r-biocmanager r-dt r-plotly r-rmarkdown r-stringi rdptools roary sickle-trim sistr_cmd spades tabulate trimmomatic; do conda install -y ${i}; done
conda list --show-channel-urls > tormes-package-list.txt

Please, share with me that tormes-package-list.txt file, so I can check the versions installed and if there were any issues.

Cheers!
Narciso

[vincenzopennone]

tormes-package-list.txt
Hi Narciso,

I have followed your guidelines and this time it seems that everything worked!
I haven't checked yet if the software actually works, I'll spend some time over the next days.
In any case, I have attached the file you requested, so you can tell me if everything actually went well or not!

Thanks a million!

Vincenzo

[nmquijada]

Hi Vincenzo,

Good that it worked!
There are a couple of software that installed in a different version than the tested ones (expected). You can try to force conda to install the same versions as the ones I tested (just to be sure):

conda activate tormes-1.3.0
conda install kraken2=2.0.9beta kaptive=0.7.3

The main issue I see is that you are still missing the installation of Mauve. Try to install it again:

conda install -c bioconda mauve mauvealigner

If that option fails (I think so, as mauvealigner is also a linux64 build), try to install it locally:

wget https://anaconda.org/bioconda/mauve/2.4.0.r4736/download/noarch/mauve-2.4.0.r4736-h9bed127_2.tar.bz2
wget https://anaconda.org/bioconda/mauvealigner/1.2.0/download/linux-64/mauvealigner-1.2.0-h6bcf2b7_2.tar.bz2
conda install -c local mauve-2.4.0.r4736-h9bed127_2.tar.bz2
conda install -c local mauvealigner-1.2.0-h6bcf2b7_2.tar.bz2

Mauve is an optional analysis for tormes (for ordering the draft genomes against a reference), but in the first steps of a tormes run, it will look for all the dependencies to be present. If one dependency is missing, it will return an error.

Let me know if you can install mauve and mauvealigner that way.

Once you have all the dependencies ready, remember to run: tormes-setup

Cheers!
Narciso

[vincenzopennone]

Hi Narciso,

Thank you for all the explanations!
It seems that everything is installed properly now, as I got this message at the end of the setup:
[TORMES]: TORMES is installed and ready to use. Enjoy!

Now I have to learn how to use it... I'll try with a few genomes to practice.

Thanks a million!

Cheers,

Vincenzo

[nmquijada]

Hi Vincenzo,

Great news! That's a good message ;)

Tormes is really easy to use (that is one of the main aims!). You just need a metadata file (https://github.com/nmquijada/tormes#obligatory-options) and you can run it as:

tormes --metadata my-metadata.txt --output out-directory

See more options that you can add to the software here

Just a some days ago, I added a shortcut on how to quickly generate metadata from a directory containing raw reads to the wiki (click here). I will update it today to show how to do so also with genomes ;)

I will close the issue now but feel free to reopen!

Best,
Narciso

[vincenzopennone]

Hi again Narciso! I tried to run tormes on a couple of isolates (one couple of reads and one assembled genome), but I get a strange error... This is what I have on the metadata file (I used the template): Samples Read1 Read2 Description Use_as_many_descrpition_colums_as_wanted Sample1 /Users/vincenzopennone/Downloads/SRR445279/SRR445279_1.fastq /Users/vincenzopennone/Downloads/SRR445279/SRR445279_2.fastq Unknown To be identified Sample2 GENOME /Users/vincenzopennone/Downloads/SRR445279/1513C.fasta Lmono Strange strain And this is the message I get when I run tormes: (tormes-1.3.0) ***@***.*** Downloads % tormes --metadata samples_metadata_prova.txt --output Prova_TORMES_2021 Thanks for using tormes version 1.3.0 Let's check that all software are properly installed and all the data included in the metadata file is correct Software ABRICATE set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/abricate Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/abricate found Software BARRNAP set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/barrnap Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/barrnap found Software CONVERT set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/convert Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/convert found Software FASTTREE set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/fasttree Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/fasttree found Software FIMTYPER set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../CGE-modules/fimtyper/fimtyper.pl Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../CGE-modules/fimtyper/fimtyper.pl found Software KAPTIVE set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/kaptive.py Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/kaptive.py found Software KRAKEN2 set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/kraken2 Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/kraken2 found Software MEGAHIT set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/megahit Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/megahit found Software MLST set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/mlst Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/mlst found Software PARALLEL set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/parallel Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/parallel found Software POINTFINDER set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../CGE-modules/pointfinder/PointFinder.py Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../CGE-modules/pointfinder/PointFinder.py found Software PRINSEQ set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/prinseq-lite.pl Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/prinseq-lite.pl found Software PRODIGAL set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/prodigal Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/prodigal found Software PROKKA set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/prokka Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/prokka found Software QUAST set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/quast Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/quast found Software RDPCLASSIFIER set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/classifier Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/classifier found Software ROARY set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/roary Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/roary found Software ROARY2SVG set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/roary2svg.pl Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/roary2svg.pl found Software RSCRIPT set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/Rscript Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/Rscript found Software SEROTYPEFINDER set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../CGE-modules/serotypefinder/serotypefinder.py Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../CGE-modules/serotypefinder/serotypefinder.py found Software SICKLE set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/sickle Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/sickle found Software SISTR set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/sistr Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/sistr found Software SPADES set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/spades.py Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/spades.py found Software TRIMMOMATIC set to: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/trimmomatic Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/trimmomatic found Software: /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../share/mauve-*/Mauve.jar found Binaries for MAUVE found Directory for /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/../db/minikraken-DB/minikraken_8GB_20200312 found Binaries for BLAST version 2.6 or later found - All the software is properly installed. - The data included in the metadata file is correct. tormes version 1.3.0 analysis will start now Status can be seen in "/Users/vincenzopennone/Downloads/Prova_TORMES_2021/tormes.log" /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/tormes: line 929: syntax error near unexpected token `>' /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/tormes: line 929: ` if ls $OUTWD/Raw_reads/*fastq &>>/dev/null; then' (tormes-1.3.0) ***@***.*** Downloads % Any idea on what's wrong here? Again, thanks for your patience! Vincenzo

…

________________________________ Da: Narciso Martin Quijada ***@***.***> Inviato: venerdì 15 ottobre 2021 12:04 A: nmquijada/tormes ***@***.***> Cc: vincenzopennone ***@***.***>; Comment ***@***.***> Oggetto: Re: [nmquijada/tormes] Installation Issue macOS BigSur (#42) Hi Vincenzo, Great news! That's a good message ;) Tormes is really easy to use (that is one of the main aims!). You just need a metadata file (https://github.com/nmquijada/tormes#obligatory-options<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnmquijada%2Ftormes%23obligatory-options&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887092380%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2FE3M3%2BXjy4ohHNJ9TYJkCYahgKA7Wxvw0DkVWhNIeMk%3D&reserved=0>) and you can run it as: tormes --metadata my-metadata.txt --output out-directory See more options that you can add to the software here<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnmquijada%2Ftormes%23usage&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887092380%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hD5WZX%2BSkxjlH48vEyEzgTx8HC9Ar%2Ff3fH4WiBgwNJQ%3D&reserved=0> Just a some days ago, I added a shortcut on how to quickly generate metadata from a directory containing raw reads to the wiki (click here<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnmquijada%2Ftormes%2Fwiki%2FShortcut-to-generate-the-metadata-file-for-TORMES&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887102372%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=75WkKesUzVcHS5fXhZy%2FtVOOrD17cuC2xHHOszYmzBE%3D&reserved=0>). I will update it today to show how to do so also with genomes ;) I will close the issue now but feel free to reopen! Best, Narciso — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnmquijada%2Ftormes%2Fissues%2F42%23issuecomment-944166711&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887102372%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=XaHGJCMFj3C6grjyJ7vywVgNM4z11waV4eCWNUqr1QU%3D&reserved=0>, or unsubscribe<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FATCVLQ5D4APUTFCXTN7AFP3UG74D7ANCNFSM5DWZQFKA&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887112369%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PuEc5njCy5153%2FRQE1V3wdxCbw7gppKrnaYHpul2yPc%3D&reserved=0>. Triage notifications on the go with GitHub Mobile for iOS<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887112369%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=swme3LPFwpvmT1DF0ET%2BsENN1IxP9DUeliANdTnPyAk%3D&reserved=0> or Android<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7C%7C63d5b64207ba4e24c19f08d98fc33899%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637698890887122364%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fJSHKtTOdydYPo8RlEbV5iinP2wS9Fr2mv93BEnu23k%3D&reserved=0>.

[nmquijada]

Hi Vincenzo,

I was very quick closing the issue hahaha
No worries, I am happy to help!

I am afraid that your error relies on the interpreter of your system... It seems that it does not recognize the &>> and this is a behavior that was introduced in bash version>4 (https://unix.stackexchange.com/questions/98062/what-is-the-use-of-in-bash).

Maybe you are running an older version of bash. Could you please run the following and let me know the output?

echo $0
echo $SHELL
which bash
bash --version

Best,
Narciso

[vincenzopennone]

Ahahah, yes, unfortunately it was too early!

This is what I got by running the scripts:
-zsh
/bin/zsh
/bin/bash
GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin20)
Copyright (C) 2007 Free Software Foundation, Inc.

So I have installed a new version and set it as default shell following the steps in this link (hopefully I didn't make it worse with this):
https://itnext.io/upgrading-bash-on-macos-7138bd1066ba

However, tormes gives me the same error, even though the bash version is now this:
-bash
/usr/local/bin/bash
/usr/local/bin/bash
GNU bash, version 5.1.8(1)-release (x86_64-apple-darwin20.3.0)
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

It seems a never-ending story... (LOL)

All the best
Vincenzo

[nmquijada]

Hi Vincenzo!

Well... programming is like the tip of an iceberg... 10% coding, 90% debugging. But we are getting closer!

Good that you updated bash in your system.
I was going to suggest you to do so via conda (https://anaconda.org/conda-forge/bash), so you don't disturb your entire system (although an update of bash was pretty much recommended in your case). If you are working with conda environments, always try to modify everything with conda, because in case of errors you can easily delete your conda environment without any repercussion to your system.

I think that the problem now is the bash that tormes is trying to use, as specified in its shebang (https://linuxize.com/post/bash-shebang/). In the scripts for tormes, I made the shebang to be /bin/bash, but in your case, bash is in /usr/local/bin/bash.

To make sure that this is the issue, can you please run the following and paste the output?

/bin/bash --version
/usr/local/bin/bash --version

Thanks!
Narciso

[vincenzopennone]

Hi Narciso!

Thanks, I'm learning a lot from this conversation!
So, running /bin/bash --version gives me:
GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin20)
Copyright (C) 2007 Free Software Foundation, Inc.

While running /usr/local/bin/bash --version gives me:
GNU bash, version 5.1.8(1)-release (x86_64-apple-darwin20.3.0)
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Regards,

Vincenzo

[nmquijada]

Hi Vincenzo,

Good. So tormes is trying to use /bin/bash which is version 3.2 (<4) and therefore fails.
When you performed the bash update in your system you did not modify /bin/bash but stored your new bash (v5.1.8) in a different location (/usr/local/bin/bash).
So your system is dealing with two bash versions. It is not a problem, but you have to be aware of this fact for the future.

So you have two options here:

• You can update bash also in /bin (note that sudo might be required). So you have the updated version of bash in the most "common" locations. However, in the last steps of your tutorial (https://itnext.io/upgrading-bash-on-macos-7138bd1066ba) it does not recommend this solution in macOS due to a macOS security feature (https://en.wikipedia.org/wiki/System_Integrity_Protection), but would be something like:

cp /bin/bash /bin/bash.old #just to keep a copy of the old bash that you can restore by: cp /bin/bash.old /bin/bash
ln -s /usr/local/bin/bash /bin/bash

• You can modify the shebang of all tormes scripts (I will include this modification in the next version, for users running into the same issue). For doing so automatically:

conda activate tormes-1.3.0
for i in $(ls $(which tormes | sed "s/$/\*/")); do sed -i "1c#! \/usr\/bin\/env bash" ${i}; done

I would say that you use the second approach (modifying tormes shebang), so you don't have to deal with this macOS (in)security stuff.

Let me know!
Narciso

[vincenzopennone]

Hi Narciso,

Yes, I didn't update bash in /bin because it was not recommended for mac...
I've run the script to modify the shebang but I get an error:

(tormes-1.3.0) MacBook-Pro-di-vincenzo:~ vincenzopennone$ for i in $(ls $(which tormes | sed "s/$/*/")); do sed -i "1c#! /usr/bin/env bash" ${i}; done
sed: 1: "/Users/vincenzopennone/ ...": invalid command code v
sed: 1: "/Users/vincenzopennone/ ...": invalid command code v
sed: 1: "/Users/vincenzopennone/ ...": invalid command code v
sed: 1: "/Users/vincenzopennone/ ...": invalid command code v
sed: 1: "/Users/vincenzopennone/ ...": invalid command code v
sed: 1: "/Users/vincenzopennone/ ...": invalid command code v

I have no idea what this means... sorry...

Cheers,

Vincenzo

[nmquijada]

Hi Vincenzo,

Oh man, another different macOS behaviour. The "-i" flag of sed that in Linux modifies the file itself requires a different coding (https://www.markhneedham.com/blog/2011/01/14/sed-sed-1-invalid-command-code-r-on-mac-os-x/).
This way of coding is repeated several times within tormes, so let's try first to install a gnu-sed

conda install -c conda-forge sed

An then run again:

for i in $(ls $(which tormes | sed "s/$/\*/")); do sed -i "1c#! \/usr\/bin\/env bash" ${i}; done

Let's see...
Narciso

[vincenzopennone]

conda install -c conda-forge sed

This gives me an error...

(base) MacBook-Pro-di-vincenzo:~ vincenzopennone$ conda install -c conda-forge sed
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /Users/vincenzopennone/miniconda

added / updated specs:
- sed

The following NEW packages will be INSTALLED:

sed conda-forge/osx-64::sed-4.7-h3efe00b_1000

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/cli/install.py", line 317, in install
    handle_txn(unlink_link_transaction, prefix, args, newenv)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/cli/install.py", line 346, in handle_txn
    unlink_link_transaction.execute()
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 245, in execute
    self.verify()
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 232, in verify
    exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 591, in _verify
    for exc in self.verify_executor.map(UnlinkLinkTransaction._verify_individual_level,
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/common/io.py", line 525, in map
    yield func(thing)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 412, in _verify_individual_level
    error_result = axn.verify()
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/core/path_actions.py", line 418, in verify
    create_link(self.source_full_path, self.intermediate_path, LinkType.copy)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/gateways/disk/create.py", line 373, in create_link
    copy(src, dst)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/gateways/disk/create.py", line 310, in copy
    _do_copy(src, dst)
  File "/Users/vincenzopennone/miniconda/lib/python3.8/site-packages/conda/gateways/disk/create.py", line 323, in _do_copy
    with open(dst, 'wb') as fdst:
PermissionError: [Errno 13] Permission denied: '/Users/vincenzopennone/miniconda/.condatmp/6751f23b-bed1-4dc4-95a5-7b92ba7288fa'

$ /Users/vincenzopennone/miniconda/bin/conda install -c conda-forge sed

environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/vincenzopennone/miniconda/bin/conda
CONDA_MKL_INTERFACE_LAYER_BACKUP=
CONDA_PREFIX=/Users/vincenzopennone/miniconda
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/Users/vincenzopennone/miniconda/bin/python
CONDA_ROOT=/Users/vincenzopennone/miniconda
CONDA_SHLVL=1
CURL_CA_BUNDLE=
JAVA_LD_LIBRARY_PATH=/Users/vincenzopennone/miniconda/lib/server
PATH=/Users/vincenzopennone/miniconda/bin:/Users/vincenzopennone/miniconda/
bin:/Users/vincenzopennone/miniconda/condabin:/usr/local/bin:/usr/bin:
/bin:/usr/sbin:/sbin:/usr/local/ncbi/blast/bin:/opt/X11/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : base
active env location : /Users/vincenzopennone/miniconda
        shell level : 1
   user config file : /Users/vincenzopennone/.condarc

populated config files : /Users/vincenzopennone/.condarc
conda version : 4.10.3
conda-build version : 3.21.4
python version : 3.8.12.final.0
virtual packages : __osx=10.16=0
__unix=0=0
__archspec=1=x86_64
base environment : /Users/vincenzopennone/miniconda (writable)
conda av data dir : /Users/vincenzopennone/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/osx-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
https://conda.anaconda.org/r/osx-64
https://conda.anaconda.org/r/noarch
https://conda.anaconda.org/anaconda/osx-64
https://conda.anaconda.org/anaconda/noarch
package cache : /Users/vincenzopennone/miniconda/pkgs
/Users/vincenzopennone/.conda/pkgs
envs directories : /Users/vincenzopennone/miniconda/envs
/Users/vincenzopennone/.conda/envs
platform : osx-64
user-agent : conda/4.10.3 requests/2.26.0 CPython/3.8.12 Darwin/20.6.0 OSX/10.16
UID:GID : 501:20
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

I have found this tutorial:
https://medium.com/@bramblexu/install-gnu-sed-on-mac-os-and-set-it-as-default-7c17ef1b8f64

But I wait for your green flag before using it!

Thanks

Vincenzo

[nmquijada]

Hi Vincenzo,

Thanks for the report. The tutorial looks fine! I was trying to do the same by using conda, but obviously it failed...
The tutorial is absolutely safe, as your main sed won't be removed (and the new gnu-sed can be removed later if not needed). If you are going to use bash tools/scripts developed under Linux you will get benefited by having gnu-sed.

Then install the gnu-sed as explained in your tutorial. Do you have experience with the bashrc file?

Best,
Narciso

[vincenzopennone]

Ok, I have used the tutorial and I got the exact outputs that were described, so I guess now I have gnu-sed installed and which sed gives me /usr/local/opt/gnu-sed/libexec/gnubin/sed
Also, typing just sed gives me the info and options of sed usage.

So, I activated the tormes environment and run
for i in $(ls $(which tormes | sed "s/$/*/")); do sed -i "1c#! /usr/bin/env bash" ${i}; done

This way, tormes seems to work!

I have tried the same example that I was running a few posts above, however, it seems that not everything worked well. The sample 1 (two read files) did not produce any output and the sample 2 (contigs) failed the annotation. No html report was produced. I attach the log file.
tormes.log

Thanks again for all your patience!

Vincenzo

[nmquijada]

Hi Vincenzo,

Could you please run this?

tormes -m samples_metadata_prova.txt -o Output-error -t 8 &>>error-tormes.txt 2>>error-tormes.txt &

By doing this, tormes will run in the background of your computer and won't see anything, but all the outputs will be stored in the file "error-tormes.txt".
You can always see the ongoing tasks on your system by typing ps -fu $USER, top or htop.
Once it's ended (will take ~6 minutes considering your last run), please share with me the error-tormes.txt file.

If you think you have sensitive information, please address me at nmartinquijada@gmail.com

Thanks!
Narciso

[vincenzopennone]

Done!

Here's the file:
error-tormes.txt

Thanks a million,

Vincenzo

[nmquijada]

Hi Vincenzo,

Thanks for sharing!
You are still having issues with sed... This is the the thing that worries me the most... because this makes other software included in tormes to also give issues... Please make sure to run this before running tormes:

export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"

The read files do not produce any output because their mean length is 50bp and by default tormes trims at 125bp. You can use the --min_len parameter for this (see below).

The annotation with Prokka is failing because of an issue with tbl2asn. We'll force to install the required version, but you can also run tormes without Prokka by using the --only_gene_prediction, but let's try to make everything work.

So, things to do:

conda activate tormes-1.3.0
rm -r Output-error
rm error-tormes.txt
conda install -y -c bioconda tbl2asn=25.7
export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
tormes -m samples_metadata_prova.txt -o Output-error -t 8 --min_len 25 --filtering trimmomatic &>>error-tormes.txt 2>>error-tormes.txt &

And please send to me this "error-tormes.txt".

Thanks,
Narciso

[vincenzopennone]

Hi Narciso,

So, the problems are not finished yet!
When I run conda install etc... I get this and the computer stalls (I stopped it after 20 minutes that it was not progressing):
(tormes-1.3.0) MacBook-Pro-di-vincenzo:SRR445279 vincenzopennone$ conda install -y -c bioconda tbl2asn=25.7
Collecting package metadata (current_repodata.json): done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

• /noarch::mauve==2.4.0.r4736=h9bed127_2

• /linux-64::mauvealigner==1.2.0=h6bcf2b7_2
  failed with initial frozen solve. Retrying with flexible solve.
  Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
  Collecting package metadata (repodata.json): done
  Solving environment: |
  The environment is inconsistent, please check the package plan carefully
  The following packages are causing the inconsistency:

• /noarch::mauve==2.4.0.r4736=h9bed127_2

• /linux-64::mauvealigner==1.2.0=h6bcf2b7_2

I'm starting thinking that tormes is not compatible with my mac...

In any case thanks, this discussion is teaching me a lot!

Vincenzo

[nmquijada]

Hi Vincenzo,

Good that you are learning! I am sorry I still did not get the clue...

You are running incompatibility issues with this mauve again... So the thing is that tormes is a pipeline that wraps the work of many other software that also require some software and dependencies. I can check what is causing errors for you with tormes, but with the other software it becomes a bit more complex.
For instance, for the annotation, Prokka is failing for you because of that tbl2asn. If you try to annotate your genome:

conda activate tormes-1.3.0
prokka Sample2.fasta --outdir Sample2-annotation --prefix Sample2 --locustag Sample2 --cpus 8 --force

You will run into an error. But this does not mean that Prokka won't work at all in your system. Maybe if you create a conda environment just with Prokka it will work. However, in the environment that you created for tormes, there are some packages that are running into conflicts in your system.
The goal of making a conda environment is to solve all this incompatibility issues. But the "standard" conda installation failed, so it is a bit complex to overcome the errors. Actually, it is pretty frustrating for me to not be able to use your computer but use this chat instead...

Can you please run this and share the "error-tormes.txt" with me please?

conda activate tormes-1.3.0
rm -r Output-error
rm error-tormes.txt
export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
tormes -m samples_metadata_prova.txt -o Output-error -t 8 --min_len 25 --filtering trimmomatic --only_gene_prediction &>>error-tormes.txt 2>>error-tormes.txt &

I will create a virtual machine mimicking your system, so I will try to reproduce the error. However, it might take time.

In the meantime... are you familiar with VirtualBox? (https://www.virtualbox.org/)
This tool allows you to create small "system configurations" of other operating system (windows, linux) within your own system. It is less efficient than using your own computer, but it has the advantage to use a different operating system and to delete the environment once you are done (or if you have errors) without repercussions to your system.
We were using this quite often some years ago under some circumstances (such as for training courses, I created a VM and everybody cloned it in their computers so we will all have the same configuration, tools, etc.).
As tormes is not very computing demanding and your computer is not a cluster one, maybe you can try to create a VM in your system with a Linux environment and install tormes (and anything you would like) inside it.
You can find a very easy tutorial here https://www.imore.com/how-use-linux-your-mac-using-virtual-machine

Best,
Narciso

[vincenzopennone]

Hi Narciso,

Here is the error file
error-tormes.txt

I will have a look about the VM, I knew about their existence to run windows on mac, but I've never thought about it with linux...
In any case, thanks a million for your effort, at least now I know that I was not doing anything wrong, I just have the wrong computer!
If you happen to be in Leòn any soon, we can arrange for you to get your hands on my computer in person, I'm pretty sure this would be much easier for you!

All the best,

Vincenzo

[nmquijada]

Hi Vincenzo,

Thanks a lot for sharing all the error files. I will consider all the issues here for a next release of tormes, where I should consider other alternatives for those having issues with conda.

You were not doing anything wrong! Do not blame your computer either... let's say we did not get the "optimal configuration". Yeah, that's polite xD Most things have solutions, but sometimes it takes longer.

I definitely encourage you to use VM. That might solve your incompatibility issues.

Regarding tormes in your computer. I see from the "error-tormes.txt" that most software run properly but you still have some issues.
One is related to a MacOS "Segmentation fault: 11" that might be solved for this if you run:

export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
sed -i 's/kraken-report.txt &>>\/dev\/null/kraken-report.txt/' /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/tormes

You are still missing one R package installation:

conda activate tormes-1.3.0
R
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggtree")
q()

The rRNA detection with Barrnap is failing due to nhmmer. There is a similar issue in its developer's page, but does not have a response yet...

Prokka is failing due to tblast2n (you can perform the gene prediction with the --only_gene_prediction, as Prodigal worked nicely). Maybe you can get tbl2asn from the NCBI repository (without conda):

wget https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/mac.tbl2asn.gz
gzip -d mac.tbl2asn.gz
mv mac.tbl2asn.gz /Users/vincenzopennone/miniconda/envs/tormes-1.3.0/bin/tbl2asn

If you happen to run all that, you can try tormes again as:

conda activate tormes-1.3.0
rm -r Output-error
rm error-tormes.txt
export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
tormes -m samples_metadata_prova.txt -o Output-error -t 8 --min_len 25 --filtering trimmomatic &>>error-tormes.txt 2>>error-tormes.txt &

I may visit León sometime, as I am working in a project with very nice people from there! I think you know them ;)

Best,
Narciso

[MinTing-limit]

Hello,
I followed your suggestion (#42 (comment)) for installing TORMES on my mac. Everything seemed to be good until I tried to install the rest of the dependencies with

for i in abricate ant biopython cgecore fasttree git imagemagick kaptive kraken2 mauve mauvealigner megahit mlst parallel perl-data-dumper perl-try-tiny bioconda::perl-try-tiny-retry prinseq prokka quast r-biocmanager r-dt r-plotly r-rmarkdown r-stringi rdptools roary sickle-trim sistr_cmd spades tabulate trimmomatic; do conda install -y ${i}; done conda list --show-channel-urls > tormes-package-list.txt

I got messages as below for each dependency:

**Channels:

• conda-forge
• bioconda
• defaults
• r
• anaconda
  Platform: osx-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

InvalidMatchSpec: Invalid spec 'tormes[url=file:///Users/min-tinglee/tormes-1.3.0-py36_0.tar.bz2]': Libmamba only supports a subset of the MatchSpec interface for now. You can only use ('name', 'version', 'build', 'channel', 'subdir'), but you tried to use ('url',).**

Could you help me resolve this? Thank you so much in advance!