Installation fails due to unsatisfiable constraints

[aneichyk]

The pipeline fails on a newly set-up Ubuntu single node server. (AWS EC2 instance) The execution command:

nextflow run nextNEOpi.nf --batchFile batchFile_s3_FASTQ.csv -config conf/params.config --outputDir /home/ubuntu/nextNEOpi_results -profile conda --accept_license 

The error message:

Error executing process > 'make_CNVkit_access_file (mkCNVkitaccess)' 
...
UnsatisfiableError: The following specifications were found to be incompatible with each other:
...

The required software and OS versions:

(base) Thu Dec 09 ~/nextNEOpi $ nextflow -version

      N E X T F L O W
      version 21.10.5 build 5658
      created 08-12-2021 14:39 UTC 
      cite doi:10.1038/nbt.3820
      http://nextflow.io

(base) Thu Dec 09 ~/nextNEOpi $ java --version
openjdk 11.0.11 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)
(base) Thu Dec 09 ~/nextNEOpi $ conda --version
conda 4.10.3
(base) Thu Dec 09 ~/nextNEOpi $ cat /etc/os-release 
NAME="Ubuntu"
VERSION="20.04.2 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.2 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal

[aneichyk]

Complete log: nextflow.log

[riederd]

Hi, thanks for opening the issue. It seems that there is a problem on your Ubuntu 20.04.2 machine to create the bioconda cnvkit env.

Can you try to verify this by running: conda create --mkdir --yes --quiet --prefix /home/ubuntu/test_cnvkit bioconda::cnvkit=0.9.9

Would it be possible for you to test the pipeline on a CentOS 7 AWS instance? We are running CentOS 7.9 locally, and there we do not see this issue. Debian 10 seem also to work.

We have to look into this, however we are not providing the bioconda packages.

[riederd]

I just checked on a vanilla Ubuntu 20.04.3 docker image and it seems that the cnvkit conda installation is working. Please make sure that you add the following conda channels before running the pipeline:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

I hope this solves your problem

[aneichyk]

[ff/c12606] process > make_CNVkit_access_file (mkCNVkitaccess) [100%] 1 of 1 ✔

Adding bioconda and conda-forge to channels solved the issue. Thanks!

[aneichyk]

Sorry, gonna reopen this one as it seems to be still issue with the environments. This time its the process RegionsBedToIntervalList Here is the message

Error executing process > 'RegionsBedToIntervalList (RegionsBedToIntervalList)'                                                                                                                                                                                                 

Caused by:                                                                                                                                                                                                                                                                      
  Failed to create Conda environment                                                                                                                                                                                                                                            
  command: conda env create --prefix /home/ubuntu/nextNEOpi/work/conda/nextNEOpi-793bd3cf3a3d634bcf12326ab71820ea --file /home/ubuntu/nextNEOpi/assets/nextNEOpi.yml                                                                                                            
  status : 143                                                                                                                                                                                                                                                                  
  message:          

[aneichyk]

Here is once again a complete log: nextflow.log

[riederd]

I'm sorry that you ran again into an issue. Can you edit the /home/ubuntu/nextNEOpi/assets/nextNEOpi.yml and replace bioconda::pysam=0.16.0.1 with bioconda::pysam=0.16

Let me know if that works

[aneichyk]

seems to have solved the installation, but I now have an issue with CPU requirements:

  Process requirement exceed available CPUs -- req: 34; avail: 16

I tried to find where task.cpus is defined, but it doesn't seem to be in the conf/ folder or in the nf file. Could you point me to where is it defined?

Do you want me to open a different issue for this?

[riederd]

please look into conf/process.config you can adjust the number of cpus there for all multithreaded processes. I think in your case it is the BWA process.

[riederd]

In the README we state:

Before running the pipeline, the config files in the conf/ directory may need to be edited. In the params.config parameters default settings are defined. The process.config is a template for the configuration of the single processes, you may check the number of CPUs assigned for each process and adjust according to your systems capabilities.

Anyway, we lower the number of cpus in that default config in the next release.

[riederd]

I'm going to close this issue for now, We just released nextNEOpi_v1.2.1 that should fix the problems. Thanks again.