Hi,
I'm new to bioinformatics. I'm having trouble installing the TB-Profiler tool (used for deducing drug susceptibility from microbial WGS data).
I used the instructions for installing the tool using Terminal (MacOs Mojave) and Anaconda.
However, I keep running into the error, 'failed with initial frozen solve' and 'Found conflicts!'
What follows is a list of just a few of the detected incompatiblities:
Apparently something has gone wrong in installing TB-Profiler and the required additional packages. And it has to do with version incompatibilities?
Does anybody recognize what has gone wrong and what can be done about it?
I wondered whether a 'clean install' of both TB-Profiler and all related modules is useful? If so, how does one do that? I didn't find a clear 'uninstalling' module for TB-Profiler in Anaconda.
When I try to use my current installation of TB-PRofiler for analysis of a fastq-file, I get this error:
This is a known bug, which could be resolved by installing a more recent version of one of the prerequisites of TB-Profiler, using this code:
(https://github.com/jodyphelan/TBProfiler/issues/39)
However, when trying to install I run into the same unsatisfiable error as described above.
Any help is much appreciated.
regards,
Klaas
I'm new to bioinformatics. I'm having trouble installing the TB-Profiler tool (used for deducing drug susceptibility from microbial WGS data).
I used the instructions for installing the tool using Terminal (MacOs Mojave) and Anaconda.
However, I keep running into the error, 'failed with initial frozen solve' and 'Found conflicts!'
Code:
conda install -c bioconda tb-profiler samtools=1.9=h7c4ea83_11 ncurses=6.1=h0a44026_1002 Collecting package metadata (current_repodata.json): done Solving environment: [B]failed with initial frozen solve. Retrying with flexible solve.[/B] Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages.
Code:
[B]UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:[/B] Specifications: - anaconda-navigator -> python[version='2.7.*|3.5.*|3.6.*|3.4.*'] - anaconda-project -> python[version='3.4.*|>=3.8,<3.9.0a0'] - anaconda==2020.02 -> python[version='3.6.10|3.7.6|3.8.1',build='h359304d_0|h359304d_1|h359304d_2'] ... - testpath -> python[version='3.4.*|>=3.8,<3.9.0a0'] - watchdog -> python[version='>=3.5,<3.6.0a0'] - zict -> python[version='>=3.8,<3.9.0a0'] Your python: python=3.7 If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that. The following specifications were found to be incompatible with each other: Output in format: Requested package -> Available versions Package python_abi conflicts for: pyflakes -> python -> python_abi[version='3.6.*|3.6|3.8.*|3.7.*',build='*_cp36m|*_cp37m|*_pypy36_pp73|*_cp38'] jupyter_core -> python_abi[version='2.7.*|3.6|3.6.*|3.8.*|3.7.*',build='*_cp37m|*_cp36m|*_pypy36_pp73|*_cp27m|*_cp38'] ...And many more
Does anybody recognize what has gone wrong and what can be done about it?
I wondered whether a 'clean install' of both TB-Profiler and all related modules is useful? If so, how does one do that? I didn't find a clear 'uninstalling' module for TB-Profiler in Anaconda.
When I try to use my current installation of TB-PRofiler for analysis of a fastq-file, I get this error:
Code:
TypeError: profiler() got an unexpected keyword argument 'af'
Code:
conda install pathogen-profiler=1.3
However, when trying to install I run into the same unsatisfiable error as described above.
Any help is much appreciated.
regards,
Klaas
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