I have installed CheckM (checkm-genome: https://github.com/Ecogenomics/CheckM/wiki) on a custom VM (hosted at Swansea), making sure to install dependencies (covered by installing with pip) and downloading the required data files as per the installation instructions on the software wiki. However when I try and run it, I get the same error:
IOError: [Errno 2] No such file or directory: u’/home/ubuntu/maxbin/hmms/phylo.hmm’
The code I am trying t run has worked for me before, on climb, using the following command:
checkm lineage_wf -t 8 -x fasta /home/ubuntu/maxbin/103_L5 /home/ubuntu/maxbin/103_L5/checkm
The error message shorts the pipeline so the analysis starts but doesn’t complete, and the outputted files are useless.
Any help on what I might be able to do to solve this problem is much appreciated!