Installation issue

[dhpalmer]

If you could please help I'd appreciate it.

When running the following:

conda install -c bioconda read2tree

I get this output and error:

Collecting package metadata (current_repodata.json): done
Solving environment: 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: failed with initial frozen solve. Retrying with flexible solve.
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 versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17

[sinamajidian]

Hi @dhpalmer

Thanks for using read2tree.

Could you please provide us more information about your system and python/conda version and the full command line you used?
We would suggest to create a new environment as described in the readme with python 3.10.

It seems that such an error may arise if you have incompatible python version as described here or outdated conda version
mentioned here.

Regards,
Sina

[bfauskee]

Hello,

I am getting the same issue on an AWS system:

conda install -c bioconda read2tree
Collecting package metadata (current_repodata.json): done
Solving environment: 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: failed with initial frozen solve. Retrying with flexible solve.
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 versionsThe following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.35=0
• feature:|@/linux-64::__glibc==2.35=0

Your installed version is: 2.35

I have conda 23.3.1 and am in an environment with python 3.10.11

[sinamajidian]

Dear @bfauskee

Thanks for reporting the issue in details. I was able to reproduce it and we will investigate the issue soon.

In the meanwhile, I would suggest to use python 3.10.8 as I just tested with a fresh environment and read2tree works well. (It may take a while for conda to resolve the environment and install read2tree).

I would appreciate it if you could inform us whether this python version works for you or not.

Regards,
Sina

[bfauskee]

Yep this worked for me. Seems to be running well on python 3.10.8. Thanks!

[CJJ8848]

Hi @sinamajidian,

I also have a trouble with the conda install. I built up a fresh env with python=3.10.8 and conda 23.3.1 in a Linux system. Here it is:

conda create -n r2t3.10.8 python=3.10.8
conda activate r2t3.10.8
(r2t3.10.8) conda install -c bioconda read2tree
Collecting package metadata (current_repodata.json): done
Solving environment: 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: failed with initial frozen solve. Retrying with flexible solve.
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 versionsThe following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.17=0
• feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17

I also tried to build read2tree from source in python 3.8 and succeded. I also succeded to run the reference with 'read2tree --standalone_path marker_genes/ --output_path output --reference' Then when I tried to run multispecies mode with the command 'read2tree --standalone_path marker_genes/ --output_path output --reads species1_R1.fastq species2_R2.fastq', it throwed an error 'ValueError: fetch called on bamfile without index' in Mapper.py 499 line. I am confused about this and have kept debugging for three days. I guess there should be some conficts happened after installing from source as well. I would aprreciate it if you could help me out.