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epi2me-labs / wf-mpx

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Fail to create conda env with yaml #3

Closed antoine4ucsd closed 2 years ago

antoine4ucsd commented 2 years ago

What happened?

Hello trying to run the workflow on the test mxp fastq. I have a Macbook Pro M2. I would like to use a conda dedicated environnment. I tried to use the yaml file but get conflicts (see log below). I also tried to install epiflow separately and ran the following command:

nextflow run epi2me-labs/wf-mpx --fastq test_data/reads.fastq.gz

but it requires docker... do you have an updated yml file to use to create a working env?

thank you!

Operating System

macOS

Workflow Execution

Other (please describe)

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

No response

Workflow Version

most recent github

Relevant log output

conda env create -f environment.yaml 
Collecting package metadata (repodata.json): done
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                                                                         -  
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                                                                         \  

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

Output in format: Requested package -> Available versions

Package bzip2 conflicts for:
pyvcf -> python=3.6 -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
mosdepth -> htslib[version='>=1.15,<1.16.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']
python=3.8 -> bzip2[version='>=1.0.8,<2.0a0']
pysam -> bzip2[version='>=1.0.8,<2.0a0']
fastcat -> htslib -> bzip2[version='1.0.*|>=1.0.6,<2.0a0']
pysam -> python[version='>=3.6,<3.7.0a0'] -> bzip2[version='1.0.*|>=1.0.6,<2.0a0']
aplanat -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
flye -> python[version='>=3.7,<3.8.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
pandas -> pypy3.9[version='>=7.3.9'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
epi2melabs -> python -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
fastcat -> bzip2[version='>=1.0.8,<2.0a0']
bedtools -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
medaka -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
pomoxis -> bcftools[version='>=1.9'] -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
vcf-annotator -> python[version='>=3'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']

Package libssh2 conflicts for:
fastcat -> libcurl[version='>=7.80.0,<8.0a0'] -> libssh2[version='>=1.10.0,<2.0a0|>=1.9.0,<2.0a0']
pysam -> libcurl[version='>=7.83.1,<8.0a0'] -> libssh2[version='1.*|>=1.10.0,<2.0a0|>=1.9.0,<2.0a0|>=1.8.0,<2.0.0a0|>=1.8.2,<2.0a0|>=1.8.0,<2.0a0']
bedtools -> curl[version='>=7.64.1,<8.0a0'] -> libssh2[version='>=1.10.0,<2.0a0|>=1.9.0,<2.0a0|>=1.8.0,<2.0.0a0|>=1.8.2,<2.0a0']

Package pyyaml conflicts for:
epi2melabs -> nf-core -> pyyaml
medaka -> keras==2.2.4 -> pyyaml
pomoxis -> watchdog -> pyyaml[version='>=3.10']
medaka -> pyyaml==5.1
aplanat -> bokeh -> pyyaml[version='>=3.10']

Package six conflicts for:
epi2melabs -> jsonschema -> six[version='>=1.11.0']
pandas -> python-dateutil[version='>=2.8.1'] -> six[version='>=1.5']
medaka -> h5py==2.7.1 -> six[version='>=1.10.0|>=1.9|>=1.9.0']
aplanat -> bokeh -> six[version='>=1.10.0|>=1.5.2']

Package libcxx conflicts for:
minimap2 -> k8 -> libcxx[version='>=11.1.0|>=12.0.1|>=9.0.1']
flye -> libcxx[version='>=11.1.0|>=12.0.1|>=9.0.1|>=4.0.1']
mosdepth -> pcre[version='>=8.45,<9.0a0'] -> libcxx[version='>=10.0.0|>=11.1.0|>=10.0.1|>=9.0.1']
vcf-annotator -> 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|>=12.0.0']
aplanat -> numpy -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=4.0.1|>=12.0.0|>=9.0.1|>=9.0.0']
pandas -> python[version='>=3.6,<3.7.0a0'] -> libcxx
pandas -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=9.0.1|>=9.0.0|>=4.0.1|>=12.0.0']
pyvcf -> python=3.6 -> 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|>=12.0.0']
pysam -> python[version='>=3.9,<3.10.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=12.0.0|>=11.1.0|>=9.0.1|>=9.0.0|>=4.0.1']
bedtools -> libcxx[version='>=11.1.0|>=12.0.1|>=9.0.1|>=4.0.1']
epi2melabs -> 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|>=12.0.0']
pomoxis -> bedtools[version='>=2.29.0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=9.0.1|>=4.0.1|>=13.0.1|>=12.0.0|>=9.0.0']
python=3.8 -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=9.0.1|>=9.0.0|>=12.0.0|>=4.0.1']
flye -> python[version='>=3.7,<3.8.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=9.0.0']
minimap2 -> libcxx[version='>=4.0.1']
medaka -> biopython -> libcxx[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=4.0.1|>=9.0.1|>=9.0.0']

Package python conflicts for:
aplanat -> bokeh -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.6|>=3.5|3.4.*|>=3.7.1,<3.8.0a0']
pomoxis -> biopython[version='>=1.63'] -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7.1,<3.8.0a0|>=3.4|3.9.10|3.8.12|3.7.12|3.7.10|3.7.10|3.6.12|3.7.9|3.6.12|3.6.9|3.6.9|3.6.9|3.6.9|<3.0.0',build='2_73_pypy|5_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|5_73_pypy|4_73_pypy|3_73_pypy|1_73_pypy|0_73_pypy']
epi2melabs -> python
pyvcf -> python_abi=3.7[build=*_cp37m] -> python[version='3.7.*|3.9.*|3.8.*']
pyvcf -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
aplanat -> python
pandas -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.*|>=3.7.1,<3.8.0a0']
vcf-annotator -> biopython -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=2.7,<2.8.0a0']
flye -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
pysam -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.*|<3.0.0']
pomoxis -> python[version='>=3.4,<3.7|>=3.6']
epi2melabs -> colorama -> python[version='2.7.*|3.5.*|3.6.*|>=3.6|3.4.*|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7|>=3.6,<4.0|>=3.5']
pysam -> python_abi=3.9[build=*_cp39] -> python[version='3.7.*|3.8.*|3.9.*']
pandas -> python-dateutil[version='>=2.8.1'] -> python[version='3.10.*|>=3|>=3.6|3.8.*|3.9.*|3.7.*']
flye -> python_abi=3.7[build=*_cp37m] -> python[version='3.4.*|3.5.*|3.6.*|3.7.*|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.10,<3.11.0a0|>=3.5,<3.6.0a0']
python=3.8
vcf-annotator -> python[version='>=3.5,<3.6.0a0|>=3|>=3.6,<3.7.0a0']

Package python-dateutil conflicts for:
epi2melabs -> nf-core -> python-dateutil
aplanat -> bokeh -> python-dateutil[version='>=2.1|>=2.8.1|>=2.7.3|>=2.6.1']
pomoxis -> matplotlib-base[version='>=3.2.1'] -> python-dateutil[version='>=2.1|>=2.7|>=2.8.1|>=2.7.3|>=2.6.1|>=2.5.*']
pandas -> python-dateutil[version='>=2.5.*|>=2.6.1|>=2.7.3|>=2.8.1']

Package setuptools conflicts for:
medaka -> whatshap==0.18 -> setuptools
pomoxis -> matplotlib-base[version='>=3.2.1'] -> setuptools[version='<60.0.0']
flye -> setuptools
pandas -> numexpr[version='>=2.7.1'] -> setuptools
python=3.8 -> pip -> setuptools
pandas -> setuptools[version='<60.0.0']
aplanat -> markdown -> setuptools[version='<60.0.0|>=36']
epi2melabs -> jsonschema -> setuptools

Package sortedcontainers conflicts for:
medaka -> intervaltree[version='>=3.0.0'] -> sortedcontainers
pomoxis -> intervaltree[version='>=3'] -> sortedcontainers
aplanat -> sigfig -> sortedcontainers

Package ca-certificates conflicts for:
flye -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
epi2melabs -> python -> ca-certificates
pysam -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python=3.8 -> openssl[version='>=1.1.1n,<1.1.2a'] -> ca-certificates
pandas -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
pyvcf -> python=2.7 -> ca-certificates
aplanat -> python -> ca-certificates

Package numpy conflicts for:
pandas -> bottleneck[version='>=1.3.1'] -> numpy[version='>=1.16.4,<2.0a0|>=1.21.3,<2.0a0']
pomoxis -> numpy[version='1.16.1|>=1.16.1']
medaka -> numpy==1.16.1
vcf-annotator -> biopython -> numpy[version='1.10.*|1.12.*|>=1.8|1.13.*|1.11.*|>=1.11.3,<2.0a0|>=1.9.3,<2.0a0']
medaka -> biopython -> numpy[version='1.10.*|1.12.*|>=1.8|1.13.*|1.11.*|>=1.11.3,<2.0a0|>=1.9.3,<2.0a0|>=1.8,<1.14|>=1.11|>=1.8.1|>=1.9.1|>=1.13.3|>=1.16.1']
pomoxis -> biopython[version='>=1.63'] -> numpy[version='1.10.*|1.12.*|>=1.8|1.13.*|1.11.*|>=1.11.3,<2.0a0|>=1.9.3,<2.0a0|>=1.17|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.15.4,<2.0a0|>=1.14.6,<2.0a0|>=1.21.2,<2.0a0|>=1.21.5,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.12.1,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.14|>=1.11.*|>=1.9.*|>=1.11|>=1.9|>=1.7|>=1.9.3,<1.10.0a0']
aplanat -> bokeh -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|>=1.11|>=1.11.3,<2.0a0|>=1.11.3|>=1.7.1|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.15.4,<2.0a0|>=1.14.6,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.21.2,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.9.3,<2.0a0|>=1.9|>=1.15.1,<2.0a0']
aplanat -> numpy
pandas -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|>=1.11|>=1.11.*|>=1.12.1,<2.0a0|>=1.14.6,<2.0a0|>=1.15.4,<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|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<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|>=1.21.2,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.11.3,<2.0a0|>=1.9.3,<1.10.0a0']

Package pkg-config conflicts for:
pysam -> samtools -> pkg-config
pomoxis -> samtools -> pkg-config

Package certifi conflicts for:
flye -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
pomoxis -> matplotlib-base[version='>=3.2.1'] -> certifi[version='>=2020.06.20']
medaka -> requests -> certifi[version='>=2017.4.17']
epi2melabs -> nf-core -> certifi[version='>=2017.4.17']
pandas -> setuptools[version='<60.0.0'] -> certifi[version='>=2016.09|>=2016.9.26']

Package libgcc conflicts for:
bedtools -> libgcc
aplanat -> scipy -> libgcc
pysam -> samtools -> libgcc
pomoxis -> racon[version='>=1.3.1'] -> libgcc
minimap2 -> libgcc

Package libopenblas conflicts for:
medaka -> numpy==1.16.1 -> libopenblas[version='>=0.3.3,<1.0a0']
medaka -> libopenblas==0.3.3

Package curl conflicts for:
fastcat -> htslib -> curl[version='>=7.59.0,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0|>=7.81.0,<8.0a0|>=7.75.0,<8.0a0|>=7.71.1,<8.0a0|>=7.78.0,<8.0a0']
pomoxis -> bcftools[version='>=1.9'] -> curl[version='>=7.59.0,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.69.1,<8.0a0|>=7.77.0,<8.0a0|>=7.81.0,<8.0a0|>=7.75.0,<8.0a0']
pysam -> curl[version='>=7.59.0,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.69.1,<8.0a0|>=7.81.0,<8.0a0|>=7.75.0,<8.0a0']
bedtools -> curl[version='>=7.64.1,<8.0a0']
medaka -> bcftools[version='>=1.9'] -> curl[version='>=7.59.0,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.69.1,<8.0a0|>=7.81.0,<8.0a0|>=7.75.0,<8.0a0']
pysam -> bcftools -> curl[version='>=7.77.0,<8.0a0|>=7.78.0,<8.0a0']

Package intervaltree conflicts for:
pomoxis -> intervaltree[version='>=3']
medaka -> intervaltree[version='>=3.0.0']

Package pypy3.6 conflicts for:
pandas -> pypy3.6[version='>=7.3.1|>=7.3.2']
flye -> setuptools -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
pyvcf -> pypy3.6[version='>=7.3.2']
vcf-annotator -> biopython -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
aplanat -> bokeh -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
medaka -> biopython -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
pyvcf -> python=3.6 -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
pomoxis -> biopython[version='>=1.63'] -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
epi2melabs -> python -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.3|>=7.3.2|>=7.3.1']
pandas -> numpy[version='>=1.19.5,<2.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.3']
pysam -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']

Package scipy conflicts for:
aplanat -> scipy
medaka -> keras==2.2.4 -> scipy[version='>=0.14']

Package libgfortran conflicts for:
aplanat -> numpy -> libgfortran[version='4.*|5.*|>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0|>=4.0.0,<5.0.0.a0']
medaka -> libopenblas==0.3.3 -> libgfortran[version='>=3.0.1,<4.0.0.a0']
pandas -> numpy[version='>=1.18.5,<2.0a0'] -> libgfortran[version='5.*|>=3.0.1,<4.0.0.a0|>=3.0,<4.0.0.a0']
bedtools -> libgcc -> libgfortran==3.0.1
minimap2 -> libgcc -> libgfortran==3.0.1
pomoxis -> numpy[version='>=1.16.1'] -> libgfortran[version='5.*|>=3.0.1,<4.0.0.a0|>=3.0,<4.0.0.a0']

Package functools32 conflicts for:
pomoxis -> matplotlib -> functools32
epi2melabs -> jsonschema -> functools32

Package libzlib conflicts for:
flye -> libzlib[version='>=1.2.11,<1.3.0a0']
pomoxis -> bcftools[version='>=1.9'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
aplanat -> pillow -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
epi2melabs -> python -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
pysam -> libzlib[version='>=1.2.11,<1.3.0a0']
vcf-annotator -> python[version='>=3'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
fastcat -> zlib -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']
bedtools -> libzlib[version='>=1.2.11,<1.3.0a0']
fastcat -> libzlib[version='>=1.2.11,<1.3.0a0']
minimap2 -> libzlib[version='>=1.2.11,<1.3.0a0']
python=3.8 -> pypy3.8=7.3.9 -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|>=1.2.12,<1.3.0a0',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']
flye -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']
pysam -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']
bedtools -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']
pandas -> pypy3.9[version='>=7.3.9'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
python=3.8 -> libzlib[version='>=1.2.11,<1.3.0a0']
pyvcf -> python=3.6 -> libzlib[version='>=1.2.11,<1.3.0a0']
mosdepth -> htslib[version='>=1.15,<1.16.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0']
minimap2 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']
medaka -> bcftools[version='>=1.9'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|>=1.2.11,<1.3.0a0',build='h6c3fc93_1014|h6c3fc93_0|hfe4f2af_1|hfe4f2af_2|h9173be1_1013|h9173be1_1012']

Package libcblas conflicts for:
pomoxis -> bcftools[version='>=1.9'] -> libcblas[version='>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
aplanat -> numpy -> libcblas[version='>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
medaka -> bcftools[version='>=1.9'] -> libcblas[version='>=3.8.0,<4.0a0']
pandas -> numpy[version='>=1.19.5,<2.0a0'] -> libcblas[version='>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']
pysam -> bcftools -> libcblas[version='>=3.8.0,<4.0a0']

Package openssl conflicts for:
bedtools -> curl[version='>=7.64.1,<8.0a0'] -> openssl[version='>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0']
epi2melabs -> 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|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1m,<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']
medaka -> python[version='>=3.6,<3.7.0a0'] -> 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|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1e,<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|>=1.0.2r,<1.0.3a']
fastcat -> htslib -> openssl[version='>=1.1.1a,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.3,<4.0a0|>=1.1.1o,<1.1.2a|>=3.0.2,<4.0a0|>=1.1.1n,<1.1.2a|>=3.0.0,<4.0a0']
pysam -> libcurl[version='>=7.83.1,<8.0a0'] -> 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|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=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|>=1.1.1b,<1.1.2a|>=1.0.2r,<1.0.3a']
vcf-annotator -> python[version='>=3'] -> 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|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1m,<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']
aplanat -> 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|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1m,<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']
pandas -> pypy3.9[version='>=7.3.9'] -> 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|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=3.0.5,<4.0a0|>=3.0.2,<4.0a0|>=3.0.3,<4.0a0|>=1.1.1o,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
pyvcf -> python=3.6 -> 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|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1e,<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|>=1.1.1k,<1.1.2a|>=1.1.1i,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1n,<1.1.2a|>=1.1.1b,<1.1.2a|>=3.0.3,<4.0a0|>=1.1.1o,<1.1.2a|>=3.0.2,<4.0a0']
flye -> python[version='>=3.7,<3.8.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<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|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1n,<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|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
python=3.8 -> pypy3.8=7.3.9 -> openssl[version='>=1.1.1q,<1.1.2a|>=3.0.5,<4.0a0']
pomoxis -> python[version='>=3.6'] -> 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|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1m,<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|>=1.0.2r,<1.0.3a']
python=3.8 -> openssl[version='>=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|>=1.1.1n,<1.1.2a|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0']

Package htslib conflicts for:
pomoxis -> bcftools[version='>=1.9'] -> htslib[version='1.3|1.3.1|1.5.*|1.6.*|1.7|1.7.*|>=1.10,<1.11.0a0|>=1.10.1,<1.11.0a0|>=1.11,<1.12.0a0|>=1.12,<1.13.0a0|>=1.13,<1.14.0a0|>=1.14,<1.15.0a0|>=1.15,<1.16.0a0|>=1.9,<1.10.0a0|>=1.10.2,<1.11.0a0|>=1.7,<1.8.0a0|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3.2,<1.4.0a0|>=1.3,<1.4|>=1.3|>=1.3.1,<1.3.2.0a0|>=1.3.1,<1.4.0a0']
medaka -> htslib[version='>=1.10.2,<1.11.0a0|>=1.9,<1.10.0a0|>=1.3.1,<1.4.0a0']
pysam -> htslib[version='1.3|1.3.1|1.5.*|1.6.*|1.7|1.7.*|>=1.7,<1.8.0a0|>=1.9,<1.10.0a0|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3.2,<1.4.0a0|>=1.3,<1.4|>=1.3|>=1.3.1,<1.3.2.0a0|>=1.3.1,<1.4.0a0']
mosdepth -> htslib[version='>=1.10.2,<1.11.0a0|>=1.11,<1.12.0a0|>=1.12,<1.13.0a0|>=1.15,<1.16.0a0|>=1.14,<1.15.0a0']
fastcat -> htslib
medaka -> bcftools[version='>=1.9'] -> htslib[version='1.3|1.3.1|1.5.*|1.6.*|1.7|1.7.*|>=1.10,<1.11.0a0|>=1.10.1,<1.11.0a0|>=1.11,<1.12.0a0|>=1.12,<1.13.0a0|>=1.13,<1.14.0a0|>=1.14,<1.15.0a0|>=1.15,<1.16.0a0|>=1.7,<1.8.0a0|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3.2,<1.4.0a0|>=1.3,<1.4|>=1.3|>=1.3.1,<1.3.2.0a0']
pysam -> bcftools -> htslib[version='>=1.10,<1.11.0a0|>=1.10.1,<1.11.0a0|>=1.11,<1.12.0a0|>=1.12,<1.13.0a0|>=1.13,<1.14.0a0|>=1.14,<1.15.0a0|>=1.15,<1.16.0a0|>=1.10.2,<1.11.0a0']

Package packaging conflicts for:
pomoxis -> matplotlib-base[version='>=3.2.1'] -> packaging[version='>=20.0']
pandas -> numexpr[version='>=2.7.1'] -> packaging
aplanat -> bokeh -> packaging[version='>=16.8']
medaka -> ont-fast5-api -> packaging
epi2melabs -> nf-core -> packaging

Package pandas conflicts for:
pandas
aplanat -> pandas[version='>=1.0.3']
aplanat -> bokeh -> pandas
pomoxis -> pandas[version='0.24.2|>=0.24.2']

Package pysam conflicts for:
pomoxis -> pysam[version='>=0.15.2']
pysam

Package h5py conflicts for:
medaka -> h5py==2.7.1
medaka -> ont-fast5-api -> h5py[version='>=2.2.1|>=2.6']

Package numpy-base conflicts for:
pandas -> numpy[version='>=1.19.5,<2.0a0'] -> 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medaka -> numpy==1.16.1 -> numpy-base==1.16.1[build='py36h6575580_0|py37ha711998_0|py27h6575580_0|py36ha711998_1|py27h6575580_1|py37h6575580_1|py37ha711998_1|py36h6575580_1|py27ha711998_1|py37h6575580_0|py27ha711998_0|py36ha711998_0']
aplanat -> 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|1.16.6|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|1.19.2|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|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.22.3|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|py27ha9ae307_6|py36ha9ae307_6|py37h9797aa9_7|py35h9797aa9_7|py27h9797aa9_7|py27h9797aa9_7|py37h9797aa9_7|py36h9797aa9_7|py27ha9ae307_7|py37ha9ae307_7|py27h9797aa9_8|py36ha9ae307_8|py36h9797aa9_8|py37ha9ae307_8|py37h9797aa9_8|py35ha9ae307_8|py37he97cb71_9|py36he97cb71_9|py27h42e5f7b_10|py36h8a80b8c_10|py35h42e5f7b_10|py27h8a80b8c_10|py35h8a80b8c_10|py27ha711998_10|py35ha711998_10|py37ha711998_10|py36ha711998_10|py37ha711998_11|py37h6575580_11|py27h6575580_11|py36h6575580_11|py37ha711998_12|py27ha711998_12|py37h6575580_12|py38ha711998_12|py38h6575580_12|py38ha711998_14|py38ha711998_15|py36h479e554_1|py35h479e554_1|py27h479e554_1|py27h7ef55bc_1|py27h9797aa9_0|py36ha9ae307_0|py35ha9ae307_0|py36ha9ae307_0|py27h9797aa9_0|py27ha9ae307_0|py36h9797aa9_1|py37h9797aa9_1|py37ha9ae307_1|py27ha9ae307_1|py37h9797aa9_2|py36h9797aa9_2|py27h9797aa9_2|py36ha9ae307_3|py36h9797aa9_3|py27ha9ae307_3|py37ha9ae307_3|py27ha9ae307_4|py36ha9ae307_4|py37ha9ae307_4|py37h9797aa9_4|py35h9797aa9_4|py35ha9ae307_4|py36ha711998_4|py27ha711998_4|py36h8a80b8c_4|py27h8a80b8c_4|py36ha711998_5|py36h6575580_5|py37ha711998_5|py37h8a80b8c_0|py27h8a80b8c_0|py36he97cb71_0|py35he97cb71_0|py36h8a80b8c_0|py36h42e5f7b_0|py27h42e5f7b_0|py27h8a80b8c_0|py37h8a80b8c_0|py37ha711998_0|py27ha711998_0|py37h8a80b8c_0|py36h8a80b8c_0|py27h8a80b8c_0|py27ha711998_1|py36ha711998_1|py27h8a80b8c_1|py37h8a80b8c_0|py37ha711998_0|py27ha711998_0|py27h8a80b8c_0|py27h8a80b8c_0|py37h8a80b8c_0|py36h8a80b8c_0|py27ha711998_0|py37ha711998_0|py27h6575580_0|py36h6575580_0|py27ha711998_0|py37h6575580_0|py27h6575580_0|py36h6575580_0|py27ha711998_1|py37h6575580_1|py36ha711998_1|py27ha711998_0|py36h6575580_0|py27h6575580_0|py37h6575580_0|py37h6575580_1|py36h6575580_0|py27h6575580_0|py37h6575580_0|py27ha711998_0|py37ha711998_0|py27h6575580_0|py27ha711998_0|py27h6575580_0|py37h6575580_0|py36h6575580_0|py27h6575580_0|py37h6575580_0|py36h6575580_0|py38h6575580_0|py38ha711998_0|py27ha711998_0|py36hd037223_3|py38hd037223_3|py36h4850c68_3|py37h4850c68_3|py38h6a6129a_4|py37hcfb5961_0|py36hcfb5961_0|py36hcfb5961_0|py38h68fea81_0|py39h3a452eb_0|py38h50ba68f_1|py39h50ba68f_1|py37h50ba68f_1|py39hf048a4f_1|py37hf048a4f_1|py39h3a452eb_0|py38h585ceec_0|py39hbbe2e76_0|py39he0bd621_0|py38hbbe2e76_0|py38hbbe2e76_0|py37he0bd621_0|py39he0bd621_0|py39he0bd621_0|py38hbbe2e76_0|py310h4c014f7_0|py310he490955_0|py39h3b1a694_1|py38h3b1a694_1|py37he782bc1_1|py39he782bc1_1|py310h6d917f3_1|py39h3b1a694_2|py38he782bc1_2|py310h6d917f3_2|py38hbda7086_3|py38h3b1a694_0|py38he782bc1_0|py39he782bc1_0|py310h6d917f3_0|py39h3b1a694_0|py310hfd2de13_0|py37hbda7086_3|py310h8a30af7_3|py39hbda7086_3|py37h3b1a694_3|py310hfd2de13_3|py39h3b1a694_3|py38h3b1a694_3|py38h3b1a694_2|py37h3b1a694_2|py37he782bc1_2|py310hfd2de13_2|py39he782bc1_2|py37h3b1a694_1|py310hfd2de13_1|py38he782bc1_1|py38he0bd621_0|py37he0bd621_0|py37hbbe2e76_0|py39hbbe2e76_0|py38he0bd621_0|py37hbbe2e76_0|py39hbbe2e76_0|py37he0bd621_0|py38he0bd621_0|py37hbbe2e76_0|py38h3a452eb_0|py37h585ceec_0|py37h3a452eb_0|py39h585ceec_0|py38hf048a4f_1|py39hde55871_0|py37h68fea81_0|py36h68fea81_0|py38hcfb5961_0|py37hcfb5961_0|py38hcfb5961_0|py37h68fea81_0|py38h68fea81_0|py36h68fea81_0|py39h6a6129a_4|py37h6a6129a_4|py38hb6794ca_4|py39hb6794ca_4|py37hb6794ca_4|py38h4850c68_3|py39h4850c68_3|py37hd037223_3|py39hd037223_3|py39h7ca7dfd_1|py39hd037223_1|py27h6575580_0|py37h6575580_0|py36ha711998_0|py37ha711998_0|py36h6575580_0|py27ha711998_0|py36ha711998_0|py37ha711998_0|py37ha711998_0|py36ha711998_0|py36h6575580_0|py37h6575580_0|py36ha711998_0|py37ha711998_0|py27ha711998_0|py36ha711998_0|py36h6575580_1|py37ha711998_1|py27ha711998_1|py27h6575580_1|py36ha711998_1|py37ha711998_0|py36ha711998_0|py36h6575580_1|py27h6575580_1|py37ha711998_1|py36ha711998_0|py37ha711998_0|py37h6575580_0|py36ha711998_0|py36h8a80b8c_0|py36ha711998_0|py37h8a80b8c_1|py36h8a80b8c_1|py37ha711998_1|py35ha711998_0|py36ha711998_0|py37ha711998_0|py35h8a80b8c_0|py35ha711998_0|py36ha711998_0|py27ha711998_0|py35h8a80b8c_0|py35h42e5f7b_0|py37h42e5f7b_0|py35h8a80b8c_0|py37he97cb71_0|py36h8a80b8c_0|py27he97cb71_0|py37h6575580_5|py27h6575580_5|py27ha711998_5|py38h6575580_4|py38ha711998_4|py37h8a80b8c_4|py37ha711998_4|py35h8a80b8c_4|py35ha711998_4|py36h9797aa9_4|py27h9797aa9_4|py37h9797aa9_3|py27h9797aa9_3|py27ha9ae307_2|py37ha9ae307_2|py36ha9ae307_2|py36ha9ae307_1|py27h9797aa9_1|py35h9797aa9_0|py35ha9ae307_0|py36h9797aa9_0|py36h9797aa9_0|py27ha9ae307_0|py35h9797aa9_0|py35h7ef55bc_1|py36h7ef55bc_1|py38h6575580_15|py38h6575580_14|py38h6575580_13|py38ha711998_13|py36ha711998_12|py27h6575580_12|py36h6575580_12|py36ha711998_11|py27ha711998_11|py36h42e5f7b_10|py37h8a80b8c_10|py37h42e5f7b_10|py35he97cb71_9|py27he97cb71_9|py35h8a80b8c_9|py36h8a80b8c_9|py27h8a80b8c_9|py37h8a80b8c_9|py35h9797aa9_8|py27ha9ae307_8|py36ha9ae307_7|py27ha9ae307_7|py36ha9ae307_7|py36h9797aa9_7|py35ha9ae307_7|py37ha9ae307_7|py37ha9ae307_6|py36h9797aa9_6|py37h9797aa9_6|py36h6575580_0|py36ha711998_0']
pomoxis -> numpy[version='>=1.16.1'] -> 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|1.16.6|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|1.19.2|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|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.22.3|1.17.0|1.17.0|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',build='py27h9797aa9_6|py36ha9ae307_6|py37h9797aa9_7|py35h9797aa9_7|py27h9797aa9_7|py27ha9ae307_7|py27h9797aa9_7|py37h9797aa9_7|py37ha9ae307_7|py27h9797aa9_8|py37ha9ae307_8|py37h9797aa9_8|py35h9797aa9_8|py35ha9ae307_8|py27he97cb71_9|py35he97cb71_9|py37h42e5f7b_10|py35h42e5f7b_10|py27h8a80b8c_10|py27ha711998_10|py35ha711998_10|py37ha711998_10|py36ha711998_10|py37ha711998_11|py37h6575580_11|py36h6575580_11|py36ha711998_12|py27ha711998_12|py38ha711998_12|py38h6575580_12|py38h6575580_13|py38ha711998_15|py35h479e554_1|py27h7ef55bc_1|py35h7ef55bc_1|py27h9797aa9_0|py36ha9ae307_0|py36h9797aa9_0|py36ha9ae307_0|py36h9797aa9_0|py27h9797aa9_0|py37h9797aa9_1|py37ha9ae307_1|py37h9797aa9_2|py36h9797aa9_2|py27h9797aa9_2|py27h9797aa9_3|py27ha9ae307_3|py37ha9ae307_3|py27h9797aa9_4|py36ha9ae307_4|py36h9797aa9_4|py37ha9ae307_4|py37h9797aa9_4|py35ha9ae307_4|py36ha711998_4|py35ha711998_4|py37ha711998_4|py27ha711998_4|py36h8a80b8c_4|py36ha711998_5|py36h6575580_5|py37ha711998_5|py37h8a80b8c_0|py27h8a80b8c_0|py35he97cb71_0|py36h8a80b8c_0|py36h42e5f7b_0|py27h42e5f7b_0|py27h8a80b8c_0|py37h8a80b8c_0|py27ha711998_0|py37h8a80b8c_0|py36h8a80b8c_0|py27ha711998_1|py36ha711998_1|py27h8a80b8c_1|py36h8a80b8c_1|py37h8a80b8c_0|py37ha711998_0|py27ha711998_0|py27h8a80b8c_0|py36h8a80b8c_0|py37h8a80b8c_0|py36h8a80b8c_0|py27ha711998_0|py37h6575580_0|py27h6575580_0|py36h6575580_0|py27ha711998_0|py37ha711998_0|py36h6575580_0|py37h6575580_1|py36h6575580_0|py27ha711998_0|py36h6575580_0|py27h6575580_0|py37h6575580_0|py37h6575580_1|py36h6575580_0|py27h6575580_0|py37h6575580_0|py27ha711998_0|py37ha711998_0|py27h6575580_0|py27ha711998_0|py27h6575580_0|py37h6575580_0|py36h6575580_0|py27h6575580_0|py37h6575580_0|py36h6575580_0|py38h6575580_0|py38ha711998_0|py27ha711998_0|py36hd037223_3|py38hd037223_3|py36h4850c68_3|py37h4850c68_3|py38h6a6129a_4|py37hcfb5961_0|py36hcfb5961_0|py36hcfb5961_0|py38h68fea81_0|py39h3a452eb_0|py38h50ba68f_1|py39h50ba68f_1|py37h50ba68f_1|py39hf048a4f_1|py37hf048a4f_1|py39h3a452eb_0|py38h585ceec_0|py39hbbe2e76_0|py39he0bd621_0|py38hbbe2e76_0|py38hbbe2e76_0|py37he0bd621_0|py39he0bd621_0|py39he0bd621_0|py38hbbe2e76_0|py310h4c014f7_0|py310he490955_0|py39h3b1a694_1|py38h3b1a694_1|py37he782bc1_1|py39he782bc1_1|py310h6d917f3_1|py39h3b1a694_2|py38he782bc1_2|py310h6d917f3_2|py38hbda7086_3|py38h3b1a694_0|py38he782bc1_0|py39he782bc1_0|py310h6d917f3_0|py39h3b1a694_0|py310hfd2de13_0|py37hbda7086_3|py310h8a30af7_3|py39hbda7086_3|py37h3b1a694_3|py310hfd2de13_3|py39h3b1a694_3|py38h3b1a694_3|py38h3b1a694_2|py37h3b1a694_2|py37he782bc1_2|py310hfd2de13_2|py39he782bc1_2|py37h3b1a694_1|py310hfd2de13_1|py38he782bc1_1|py38he0bd621_0|py37he0bd621_0|py37hbbe2e76_0|py39hbbe2e76_0|py38he0bd621_0|py37hbbe2e76_0|py39hbbe2e76_0|py37he0bd621_0|py38he0bd621_0|py37hbbe2e76_0|py38h3a452eb_0|py37h585ceec_0|py37h3a452eb_0|py39h585ceec_0|py38hf048a4f_1|py39hde55871_0|py37h68fea81_0|py36h68fea81_0|py38hcfb5961_0|py37hcfb5961_0|py38hcfb5961_0|py37h68fea81_0|py38h68fea81_0|py36h68fea81_0|py39h6a6129a_4|py37h6a6129a_4|py38hb6794ca_4|py39hb6794ca_4|py37hb6794ca_4|py38h4850c68_3|py39h4850c68_3|py37hd037223_3|py39hd037223_3|py39h7ca7dfd_1|py39hd037223_1|py27h6575580_0|py37h6575580_0|py36ha711998_0|py37ha711998_0|py36h6575580_0|py27ha711998_0|py36ha711998_0|py37ha711998_0|py37ha711998_0|py36ha711998_0|py36h6575580_0|py37h6575580_0|py36ha711998_0|py37ha711998_0|py27ha711998_0|py36ha711998_0|py36h6575580_1|py37ha711998_1|py27ha711998_1|py27h6575580_1|py36ha711998_1|py37ha711998_0|py36ha711998_0|py36ha711998_0|py36h6575580_1|py27h6575580_1|py37ha711998_1|py36ha711998_1|py27ha711998_1|py27h6575580_0|py36ha711998_0|py37h6575580_0|py37ha711998_0|py36ha711998_0|py27h8a80b8c_0|py36ha711998_0|py37h8a80b8c_1|py37ha711998_1|py35ha711998_0|py36ha711998_0|py27h8a80b8c_0|py37ha711998_0|py35h8a80b8c_0|py37ha711998_0|py35ha711998_0|py36ha711998_0|py27ha711998_0|py35h8a80b8c_0|py35h42e5f7b_0|py37h42e5f7b_0|py35h8a80b8c_0|py36he97cb71_0|py37he97cb71_0|py36h8a80b8c_0|py27he97cb71_0|py37h6575580_5|py27h6575580_5|py27ha711998_5|py38h6575580_4|py38ha711998_4|py27h8a80b8c_4|py37h8a80b8c_4|py35h8a80b8c_4|py35h9797aa9_4|py27ha9ae307_4|py37h9797aa9_3|py36h9797aa9_3|py36ha9ae307_3|py27ha9ae307_2|py37ha9ae307_2|py36ha9ae307_2|py36ha9ae307_1|py27ha9ae307_1|py36h9797aa9_1|py27h9797aa9_1|py35h9797aa9_0|py35ha9ae307_0|py27ha9ae307_0|py35ha9ae307_0|py27ha9ae307_0|py35h9797aa9_0|py27h479e554_1|py36h479e554_1|py36h7ef55bc_1|py38h6575580_15|py38h6575580_14|py38ha711998_14|py38ha711998_13|py37h6575580_12|py37ha711998_12|py27h6575580_12|py36h6575580_12|py27h6575580_11|py36ha711998_11|py27ha711998_11|py36h42e5f7b_10|py37h8a80b8c_10|py35h8a80b8c_10|py36h8a80b8c_10|py27h42e5f7b_10|py36he97cb71_9|py35h8a80b8c_9|py36h8a80b8c_9|py27h8a80b8c_9|py37h8a80b8c_9|py37he97cb71_9|py36h9797aa9_8|py36ha9ae307_8|py27ha9ae307_8|py36ha9ae307_7|py27ha9ae307_7|py36h9797aa9_7|py36ha9ae307_7|py36h9797aa9_7|py35ha9ae307_7|py37ha9ae307_7|py37ha9ae307_6|py36h9797aa9_6|py37h9797aa9_6|py27ha9ae307_6']

Package wheel conflicts for:
python=3.8 -> pip -> wheel
medaka -> parasail-python -> wheel

Package tzdata conflicts for:
pandas -> python[version='>=3.9,<3.10.0a0'] -> tzdata
epi2melabs -> python -> tzdata
vcf-annotator -> python[version='>=3'] -> tzdata
aplanat -> python -> tzdata
pyvcf -> python[version='>=3.9,<3.10.0a0'] -> tzdata
pysam -> python[version='>=3.9,<3.10.0a0'] -> tzdata
pomoxis -> python[version='>=3.6'] -> tzdata

Package libcurl conflicts for:
fastcat -> libcurl[version='>=7.80.0,<8.0a0']
pomoxis -> pysam[version='>=0.15.2'] -> libcurl[version='>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.79.1,<8.0a0|>=7.81.0,<8.0a0|>=7.82.0,<8.0a0|>=7.83.1,<8.0a0']
pysam -> libcurl[version='>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.79.1,<8.0a0|>=7.81.0,<8.0a0|>=7.82.0,<8.0a0|>=7.83.1,<8.0a0']
medaka -> htslib[version='>=1.10.2,<1.11.0a0'] -> libcurl[version='>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.83.1,<8.0a0|>=7.82.0,<8.0a0|>=7.81.0,<8.0a0|>=7.79.1,<8.0a0|>=7.75.0,<8.0a0|>=7.69.1,<8.0a0']
pysam -> 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|7.79.1|7.79.1|7.80.0|7.80.0|7.80.0|7.80.0|7.81.0|7.81.0|7.82.0|7.82.0|7.83.0|7.83.0|7.83.1|7.83.0|7.82.0|7.80.0|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|>=7.77.0,<8.0a0|>=7.64.1,<8.0a0',build='hf30b1f0_0|h051b688_0|h051b688_0|h051b688_1000|h051b688_2|h051b688_0|h051b688_0|h051b688_0|h051b688_0|h8a08a2b_0|h8a08a2b_1|h6dfd666_0|h6dfd666_0|h76de61e_1002|h76de61e_1000|h76de61e_1000|h76de61e_0|he376013_2|hc0b9707_5|h16faf7d_0|hc0b9707_1|h16faf7d_0|hc0b9707_1|hc0b9707_0|he6690cf_0|he6690cf_0|h9bf37e3_6|h9bf37e3_8|h8ef9fac_1|hf45b732_0|hf45b732_1|h97da3c1_1|h97da3c1_0|h97da3c1_1|hf45b732_0|h97da3c1_0|h23f1065_0|h372c54d_0|h23f1065_0|h372c54d_0|h9dce1e3_0|h9f20792_0|hf45b732_1|hf45b732_0|hf45b732_0|hf45b732_0|hf45b732_0|hf45b732_2|h8ef9fac_0|h8ef9fac_0|h8ef9fac_0|h9bf37e3_5|he6690cf_4|he6690cf_1|h709d2b2_0|h16faf7d_0|h16faf7d_4|hbdb9355_0|hbdb9355_0|hbdb9355_2|h6dfd666_0|hb8e4fae_0|hb8e4fae_2|h051b688_0|h051b688_0|hf30b1f0_0|hf30b1f0_0|hf30b1f0_0|hf30b1f0_0|hf30b1f0_0']
mosdepth -> htslib[version='>=1.15,<1.16.0a0'] -> libcurl[version='>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.81.0,<8.0a0|>=7.82.0,<8.0a0|>=7.79.1,<8.0a0']
bedtools -> curl[version='>=7.64.1,<8.0a0'] -> libcurl[version='7.64.1|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|7.79.1|7.79.1|7.80.0|7.80.0|7.80.0|7.80.0|7.81.0|7.81.0|7.82.0|7.82.0|7.83.0|7.83.0|7.83.1|7.83.0|7.82.0|7.80.0|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',build='h051b688_0|h051b688_0|h051b688_0|h8a08a2b_0|h8a08a2b_1|h6dfd666_0|h6dfd666_0|h16faf7d_0|hc0b9707_1|h16faf7d_0|hc0b9707_1|hc0b9707_0|he6690cf_0|he6690cf_0|h9bf37e3_6|h9bf37e3_8|h8ef9fac_1|hf45b732_0|hf45b732_1|h97da3c1_1|h97da3c1_0|h97da3c1_1|hf45b732_0|h97da3c1_0|h23f1065_0|h372c54d_0|h23f1065_0|h372c54d_0|h9dce1e3_0|h9f20792_0|hf45b732_1|hf45b732_0|hf45b732_0|hf45b732_0|hf45b732_0|hf45b732_2|h8ef9fac_0|h8ef9fac_0|h8ef9fac_0|h9bf37e3_5|he6690cf_4|he6690cf_1|h709d2b2_0|h16faf7d_0|h6dfd666_0|hb8e4fae_0|hb8e4fae_2|h051b688_0|h051b688_0|h051b688_0']
fastcat -> htslib -> libcurl[version='>=7.64.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0|>=7.79.1,<8.0a0|>=7.81.0,<8.0a0|>=7.82.0,<8.0a0']

Package requests conflicts for:
medaka -> requests
aplanat -> bokeh -> requests[version='>=1.2.3|>=2.12.5']
epi2melabs -> requests

Package biopython conflicts for:
medaka -> whatshap==0.18 -> biopython[version='>=1.73']
medaka -> biopython

Package gmp conflicts for:
bedtools -> libgcc -> gmp[version='>=4.2']
minimap2 -> libgcc -> gmp[version='>=4.2']

Package libcxxabi conflicts for:
flye -> 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|0|4|3|2|1|hebd6815_0']
bedtools -> 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|0|4|3|2|1|hebd6815_0']
pandas -> 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|0|4|3|2|1|hebd6815_0']
minimap2 -> 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|0|4|3|2|1|hebd6815_0']
python=3.8 -> 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|0|4|3|2|1|hebd6815_0']

Package mmtf-python conflicts for:
pomoxis -> biopython[version='>=1.63'] -> mmtf-python
medaka -> biopython -> mmtf-python
vcf-annotator -> biopython -> mmtf-python

Package idna conflicts for:
medaka -> requests -> idna[version='>=2.5,<2.6|>=2.5,<2.7|>=2.5,<2.8|>=2.5,<2.9|>=2.5,<3|>=2.5,<4']
epi2melabs -> nf-core -> idna[version='>=2.5,<2.6|>=2.5,<2.7|>=2.5,<2.8|>=2.5,<2.9|>=2.5,<3|>=2.5,<4']

Package matplotlib conflicts for:
pysam -> bcftools -> matplotlib
pomoxis -> matplotlib[version='3.0.3|>=3.0.3']
aplanat -> bokeh -> matplotlib

Package expat conflicts for:
pandas -> pypy3.9[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<3.0.0a0']
pyvcf -> pypy3.6[version='>=7.3.2'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.2.9,<3.0.0a0']
python=3.8 -> pypy3.8=7.3.9 -> expat[version='>=2.4.7,<3.0a0|>=2.4.8,<3.0a0']

Package bedtools conflicts for:
pomoxis -> bedtools[version='2.29.0|>=2.29.0']
bedtools

Package libnghttp2 conflicts for:
fastcat -> libcurl[version='>=7.80.0,<8.0a0'] -> libnghttp2[version='>=1.43.0,<2.0a0|>=1.47.0,<2.0a0|>=1.46.0,<2.0a0']
pysam -> libcurl[version='>=7.83.1,<8.0a0'] -> libnghttp2[version='>=1.41.0,<2.0a0|>=1.43.0,<2.0a0|>=1.46.0,<2.0a0|>=1.47.0,<2.0a0']

Package pyvcf conflicts for:
pyvcf
vcf-annotator -> pyvcf

Package zlib conflicts for:
medaka -> zlib[version='>=1.2.11,<1.3.0a0']
medaka -> mappy -> zlib[version='1.2.*|1.2.11|1.2.11.*|1.2.8.*|1.2.8']

Package minimap2 conflicts for:
pomoxis -> minimap2[version='2.17|>=2.17']
minimap2

Package xz conflicts for:
medaka -> python[version='>=3.6,<3.7.0a0'] -> xz[version='5.2.*|>=5.2.3,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
medaka -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']

Package pillow conflicts for:
aplanat -> pillow
aplanat -> bokeh -> pillow[version='>=4.0.0|>=4.0|>=7.1.0']
pomoxis -> matplotlib-base[version='>=3.2.1'] -> pillow[version='>=6.2.0']

Package jinja2 conflicts for:
aplanat -> bokeh -> jinja2[version='>=2.7|>=2.9']
epi2melabs -> nf-core -> jinja2

Package libdeflate conflicts for:
medaka -> libdeflate[version='>=1.0,<1.1.0a0|>=1.3,<1.4.0a0']
medaka -> htslib[version='>=1.10.2,<1.11.0a0'] -> libdeflate[version='>=1.10,<1.11.0a0|>=1.6,<1.7.0a0|>=1.9,<1.10.0a0|>=1.7,<1.8.0a0|>=1.5,<1.6.0a0']
mattdmem commented 2 years ago

Hello @antoine4ucsd,

Does this work?

nextflow run epi2me-labs/wf-mpx --fastq test_data/reads.fastq.gz -profile conda

Thanks

Matt

antoine4ucsd commented 2 years ago

after activate my nextflow env, I ran your suggested cmd line and got this error

nextflow run epi2me-labs/wf-mpx --fastq test_data/reads.fastq.gz -profile conda
N E X T F L O W  ~  version 21.10.6
Launching `epi2me-labs/wf-mpx` [insane_elion] - revision: 038b325037 [master]
Core Nextflow options
  revision     : master
  runName      : insane_elion
  launchDir    : /Users/me/Dropbox/_mxpv/wf-mpx-master
  workDir      : /Users/me/Dropbox/_mxpv/wf-mpx-master/work
  projectDir   : /Users/me/.nextflow/assets/epi2me-labs/wf-mpx
  userName     : me
  profile      : conda
  configFiles  : /Users/me/.nextflow/assets/epi2me-labs/wf-mpx/nextflow.config, /Users/me/Dropbox/_mxpv/wf-mpx-master/nextflow.config

Basic Input/Output Options
  fastq        : test_data/reads.fastq.gz

Meta Data
  disable_ping : false

Other parameters
  process_label: wfmpx

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-mpx for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

[-        ] process > start_ping:pingMessage  -
[-        ] process > handleSingleFile        -
[-        ] process > pipeline:summariseReads -
[-        ] process > pipeline:alignReads     -
[-        ] process > pipeline:coverageCalc   -
[-        ] process > pipeline:medakaVariants -
[-        ] process > pipeline:makeConsensus  -
[-        ] process > pipeline:getVersions    -
[-        ] process > pipeline:getParams      -
[-        ] process > pipeline:flyeAssembly   -
[-        ] process > pipeline:makeReport     -
[-        ] process > output                  -
[-        ] process > end_ping:pingMessage    -
Checking fastq input.
Single file input detected.
Creating env using mamba: /Users/me/.nextflow/assets/epi2me-labs/wf-mpx/environment.yaml [cache /Users/me/Dropbox/_mxpv/wf-mpx-master/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01]
WARN: Output `set` must define at least two component -- Check process `pipeline:coverageCalc`
Error executing process > 'handleSingleFile (1)'

Caused by:
  Failed to create Conda environment
  command: mamba env create --prefix /Users/me/Dropbox/_mxpv/wf-mpx-master/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01 --file /Users/me/.nextflow/assets/epi2me-labs/wf-mpx/environment.yaml
  status : 1
  message:
    Traceback (most recent call last):
      File "/Users/me/opt/miniconda3/bin/mamba", line 11, in <module>
        sys.exit(main())
      File "/Users/me/opt/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 882, in main
        from conda.common.compat import ensure_text_type, init_std_stream_encoding
    ImportError: cannot import name 'init_std_stream_encoding' from 'conda.common.compat' (/Users/me/opt/miniconda3/lib/python3.9/site-packages/conda/common/compat.py)
mattdmem commented 2 years ago

I think there is an issue with conda/mamba - there is an issue here that could be of help: https://github.com/mamba-org/mamba/issues/1706

You could try:

conda remove mamba
conda install mamba conda=4.12.0 -c conda-forge

I tried this but then I get a new error

from conda._vendor.auxlib.ish import dals
ModuleNotFoundError: No module named 'conda._vendor.auxlib'

Is there any reason why you can't use docker?

Thanks

Matt

antoine4ucsd commented 2 years ago

ok. I will try this. as for your question regarding docker: the only (bad) reason is that I am not familiar with it. If I cannot fix my conda env issue, I will try to learn how to use Docker.

thank you for being responsive.

mattdmem commented 2 years ago

Not a bad reason - all you have to do is install the docker desktop app for MacOS and that's all you need to do!

I just got my mamba working by doing this:

conda activate base
conda install conda=4.12

Try that too! Let me know how you get on and if you can get it working in conda or if you decide to try docker!

antoine4ucsd commented 2 years ago

I will keep you posted asap

MantaRay87 commented 2 years ago

Hey!

I am having a similar issue when running the wf via the conda profile (unfourtunatly our institution does not let us use docker, therefore I depend on the conda wf)

When running the command: nextflow run epi2me-labs/wf-mpx -profile conda --fastq ./input/ --out_dir ./output/

I get the following message:

N E X T F L O W  ~  version 22.04.0
Launching (https://github.com/epi2me-labs/wf-mpx) [evil_avogadro] DSL2 - revision: 038b325037 [master]
Core Nextflow options
  revision     : master
  runName      : evil_avogadro
  launchDir    : /MPOX/epi2me_labs_wf-mpx/run220713_Gridion_test/Congo_sample
  workDir      :/MPOX/epi2me_labs_wf-mpx/run220713_Gridion_test/Congo_sample/work
  projectDir   : /home/User/.nextflow/assets/epi2me-labs/wf-mpx
  userName     : User
  profile      : conda
  configFiles  : /home/User/.nextflow/assets/epi2me-labs/wf-mpx/nextflow.config`

Basic Input/Output Options
  out_dir      : ./output/
  fastq        : ./input/

Meta Data
  disable_ping : false

Other parameters
  process_label: wfmpx

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-mpx for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

[-        ] process > start_ping:pingMessage  -
[-        ] process > start_ping:pingMessage  -
[-        ] process > start_ping:pingMessage  [  0%] 0 of 1
[-        ] process > pipeline:summariseReads [  0%] 0 of 1
executor >  local (4)
[bc/6fc768] process > start_ping:pingMessage (1)  [  0%] 0 of 1
executor >  local (4)
[bc/6fc768] process > start_ping:pingMessage (1)  [  0%] 0 of 1
[9f/61a8ee] process > pipeline:summariseReads (1) [  0%] 0 of 1
[-        ] process > pipeline:alignReads         -
[-        ] process > pipeline:coverageCalc       -
[-        ] process > pipeline:medakaVariants     -
[-        ] process > pipeline:makeConsensus      -
[61/7eeec9] process > pipeline:getVersions        [  0%] 0 of 1
[b9/df411a] process > pipeline:getParams          [  0%] 0 of 1
[-        ] process > pipeline:flyeAssembly       -
[-        ] process > pipeline:makeReport         -
[-        ] process > output                      -
[-        ] process > end_ping:pingMessage        -
Checking fastq input.
Single directory input detected.
Creating env using mamba: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/environment.yaml [cache /MPOX/epi2me_labs_wf-mpx/run220713_Gridion_test/Congo_sample/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01]
executor >  local (4)
[bc/6fc768] process > start_ping:pingMessage (1)  [200%] 2 of 1, failed: 2 ✘
[9f/61a8ee] process > pipeline:summariseReads (1) [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:alignReads         -
[-        ] process > pipeline:coverageCalc       -
[-        ] process > pipeline:medakaVariants     -
[-        ] process > pipeline:makeConsensus      -
[61/7eeec9] process > pipeline:getVersions        [200%] 2 of 1, failed: 2 ✘
[b9/df411a] process > pipeline:getParams          [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:flyeAssembly       -
[-        ] process > pipeline:makeReport         -
[-        ] process > output                      -
[-        ] process > end_ping:pingMessage        -
Checking fastq input.
Single directory input detected.
Creating env using mamba: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/environment.yaml [cache /MPOX/epi2me_labs_wf-mpx/run220713_Gridion_test/Congo_sample/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01]
WARN: Output `set` must define at least two component -- Check process `pipeline:coverageCalc`
Error executing process > 'pipeline:getParams'

Caused by:
  Process `pipeline:getParams` terminated with an error exit status (1)

Command executed:

  # Output nextflow params object to JSON
      echo '{
      "help": false,
      "fastq": "./input/",
      "out_dir": "./output/",
      "sample": null,
      "sample_sheet": null,
      "sanitize_fastq": false,
      "wfversion": "v0.0.4",
      "threads": 4,
      "assembly": true,
      "medaka_options": null,
      "min_coverage": 20,
      "aws_image_prefix": null,
      "aws_queue": null,
      "report_name": "report",
      "disable_ping": false,
      "process_label": "wfmpx",
      "monochrome_logs": false,
      "validate_params": true,
      "show_hidden_params": false,
      "schema_ignore_params": "show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion,wf,process_label",
      "wf": {
          "example_cmd": [
              "--fastq test_data/reads.fastq.gz"
          ]
      },
      "_reference": "/home/User/.nextflow/assets/epi2me-labs/wf-mpx/./data/references/MT903344.1.fasta",
      "_genbank": "/home/User/.nextflow/assets/epi2me-labs/wf-mpx/./data/references/MT903344.1.gb"
  }' > params.json

Command exit status:
  1

Command output:
  (empty)

Command wrapper:
  Not a conda environment: /User/MPOX/epi2me_labs_wf-mpx/run220713_Gridion_test/Congo_sample/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01

Work dir:
  /MPOX/epi2me_labs_wf-mpx/run220713_Gridion_test/Congo_sample/work/b9/df411ab86b0b5379bb9641760117d8

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh``

I than tried to run the test data set directly from the nextflow environment:

`(nextflow) User:~/.nextflow/assets/epi2me-labs/wf-mpx> nextflow run epi2me-labs/wf-mpx --fastq test_data/fastq/barcode01/ -profile conda
N E X T F L O W  ~  version 22.04.0
Launching `https://github.com/epi2me-labs/wf-mpx` [scruffy_perlman] DSL2 - revision: 038b325037 [master]
Core Nextflow options
  revision     : master
  runName      : scruffy_perlman
  launchDir    : /home/User/.nextflow/assets/epi2me-labs/wf-mpx
  workDir      : /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work
  projectDir   : /home/User/.nextflow/assets/epi2me-labs/wf-mpx
  userName     : User
  profile      : conda
  configFiles  : /home/User/.nextflow/assets/epi2me-labs/wf-mpx/nextflow.config

Basic Input/Output Options
  fastq        : test_data/fastq/barcode01/

Meta Data
  disable_ping : false

Other parameters
  process_label: wfmpx

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-mpx for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

executor >  local (4)
executor >  local (4)
[96/5b1ee3] process > start_ping:pingMessage (1)  [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:summariseReads (1) -
[-        ] process > pipeline:alignReads         -
[-        ] process > pipeline:coverageCalc       -
[-        ] process > pipeline:medakaVariants     -
[-        ] process > pipeline:makeConsensus      -
[ce/74df3b] process > pipeline:getVersions        [100%] 1 of 1, failed: 1 ✘
[76/eb65b6] process > pipeline:getParams          [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:flyeAssembly       -
[-        ] process > pipeline:makeReport         -
[-        ] process > output                      -
[-        ] process > end_ping:pingMessage        -
Checking fastq input.
Single directory input detected.
Creating env using mamba: /home/ad/zrz-beca/.nextflow/assets/epi2me-labs/wf-mpx/environment.yaml [cache /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01]
WARN: Output `set` must define at least two component -- Check process `pipeline:coverageCalc`
WARN: Unable to fetch attribute for file: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01 - Hash is inferred from Git repository commit Id
WARN: Unable to fetch attribute for file: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01 - Hash is inferred from Git repository commit Id
WARN: Unable to fetch attribute for file: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01 - Hash is inferred from Git repository commit Id
WARN: Unable to fetch attribute for file: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01 - Hash is inferred from Git repository commit Id
Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (1)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  medaka --version | sed 's/ /,/' >> versions.txt
  bedtools --version | sed 's/ /,/' >> versions.txt
  flye --version | sed 's/^/flye,/' >> versions.txt
  bcftools --version | head -1 | sed 's/ /,/' >> versions.txt

Command exit status:
  1

Command output:
  (empty)

Command wrapper:
  Not a conda environment: /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/conda/epi2melabs-wf-mpx-802521f0eaf1dd7830efb72ec6467b01

Work dir:
  /home/User/.nextflow/assets/epi2me-labs/wf-mpx/work/ce/74df3bbe3e6451ad19c0cd6497a302

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run``

I was hoping, as you are looking into conda issues with the wf you would also be able to help me.

Thanks so much!

mattdmem commented 2 years ago

Hi @MantaRay87 - I'm not convinced it's the same issue, but please try my suggestions above and see if that works. @antoine4ucsd's problem is related to an issue with conda and not the workflow itself.

Thanks

Matt

antoine4ucsd commented 2 years ago

(I confirm it is a conda issue for me - works with docker...) thank you Matt.

mattdmem commented 2 years ago

great to hear @antoine4ucsd - please let me know how you get on with the workflow, if you have any comments or suggestions for improvements please drop me an email, it's relatively new and therefore we are still fine tuning to users needs.

matt dot parker at nanoporetech dot com

Thanks

@MantaRay87 - if you are still having an issue can you please open a new one? I did think after I replied that you could possibly try singularity as the profile - most institutions support it as an alternative to docker!