Open PKuperus opened 3 years ago
Hi @PKuperus,
Thanks for reporting! The key line in the error message seems to be
error: [Errno 2] No such file or directory: 'make': 'make'
.
You can install make
by apt-get -y install make
or sudo apt-get install build-essential
(I took this answer from here).
after installing make
see if it works and let me know.
I will in the meantime have a look at what makes parasail
cause this trouble.
Best, K
The build-essential
builds other things as well which you might need for parasail, so if apt-get -y install make
does not do it, maybe the heat weight build-essential
will.
I was also looking at more recent issues on the parasail repository, and observed this one: https://github.com/jeffdaily/parasail/issues/87. Where it is suggested to run sudo apt update; sudo apt install autoconf automake libtool
. Let me know how it goes.
thank you! I will try now.
...ill start with sudo apt-get install build-essential
great, I think "sudo apt-get install build-essential" worked...but still an error, as far as I understand the error...something with a incompatibl new version of pysam==0.15.2
pip install NGSpeciesID Collecting NGSpeciesID Using cached NGSpeciesID-0.1.1.1-py2.py3-none-any.whl Collecting parasail==1.1.11 Using cached parasail-1.1.11.tar.gz (46 kB) Collecting edlib>=1.1.2 Using cached edlib-1.3.8.post2-cp36-cp36m-manylinux2010_x86_64.whl (304 kB) Requirement already satisfied: numpy in ./miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1) Building wheels for collected packages: parasail Building wheel for parasail (setup.py) ... done Created wheel for parasail: filename=parasail-1.1.11-py2.py3-none-linux_x86_64.whl size=13863996 sha256=e7b2077b7f532626a11eb40b6cf43f37a7484887357cb32041618a2ddc1a87ed Stored in directory: /home/data/.cache/pip/wheels/86/9f/57/e4b92eb9286a92d9e461327be0860a7d531bcadce88ec9871c Successfully built parasail Installing collected packages: parasail, edlib, NGSpeciesID Attempting uninstall: parasail Found existing installation: parasail 1.2.4 Uninstalling parasail-1.2.4: Successfully uninstalled parasail-1.2.4 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. medaka 0.11.5 requires pysam==0.15.2, but you have pysam 0.16.0.1 which is incompatible. Successfully installed NGSpeciesID-0.1.1.1 edlib-1.3.8.post2 parasail-1.1.11
Ok good. Could you try removing the conda environment you previously set up for NGSpeciesID
completely (with the erroneous parasail) and then do a fresh install?
conda deactivate NGSpeciesID
conda env remove --name NGSpeciesID
// then install from scratch
The problem seems to be that you have some other program in your environment using a newer version of pysam. Creating a new environment in conda for NGSpeciesID and not installing any other software using pysam in this specific conda environment should hopefully fix this.
Okay: conda deactivate NGSpeciesID conda env remove --name NGSpeciesID
conda create -n NGSpeciesID python=3.6 pip conda activate NGSpeciesID conda install --yes -c conda-forge -c bioconda medaka=0.11.5 openblas==0.3.3 spoa racon minimap2 pip install NGSpeciesID
To bad! the pysam0.16.0.1 is still there
error: pip install NGSpeciesID Collecting NGSpeciesID Using cached NGSpeciesID-0.1.1.1-py2.py3-none-any.whl Collecting parasail==1.1.11 Using cached parasail-1.1.11-py2.py3-none-linux_x86_64.whl Collecting edlib>=1.1.2 Using cached edlib-1.3.8.post2-cp36-cp36m-manylinux2010_x86_64.whl (304 kB) Requirement already satisfied: numpy in ./miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1) Installing collected packages: parasail, edlib, NGSpeciesID Attempting uninstall: parasail Found existing installation: parasail 1.2.4 Uninstalling parasail-1.2.4: Successfully uninstalled parasail-1.2.4 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. medaka 0.11.5 requires pysam==0.15.2, but you have pysam 0.16.0.1 which is incompatible. Successfully installed NGSpeciesID-0.1.1.1 edlib-1.3.8.post2 parasail-1.1.11
Ok, I will look into this soon.
Reading from the log, it seems that you have NGSpeciesID
installed now (just not the medaka module). In that case, NGSpeciesID
can be run with racon
instead of medaka
for polishing. This is specified with:
NGSpeciesID --ont --consensus --racon --racon_iter 3 --fastq [reads.fastq] --outfolder [/path/to/output]
Thank you so much for your help!
...and about the pysam0.16.0.1 thingy... When I installed NGSpecieID on our second computer I noticed that pysam 0.16.0.1 gets installed during the execution of the "conda install --yes -c conda-forge -c bioconda medaka=0.11.5 openblas==0.3.3 spoa racon minimap2" command!
kind regards, Peter
Hi,
We really would like to test and use your program, but we encounter some problems with installing it. It seems like the same problem that 2tony2 mentioned. So we tried his suggestion and installed (with sudo apt) m4, autoconf, automake, libtool. Unfortunately it still doesn't work. We run it on ubuntu 20.05 (fully updated), with miniconda. Running on Win10-WSL.
Could you maybe help us out?
kind regards, Peter
The error message is copy-pasted below: