10. Troubleshooting
It may happen that the pipeline returns errors stating that certain python or R packages are not found even though the SPACCa conda environment is loaded.
To solve this problem it is sufficient to unload all the conda environments (including the base one) by typing conda deactivate until all the environment are detached: your.name@server:~$
Now load again the ChIP pipeline environment by typing conda activate SPACCa.
Check then that the pipeline is using the correct python version by typing which python.
The command should return something like /home/your.name/.conda/envs/SPACCa/bin/python instead of /usr/bin/python.
In particular for the variant calling, pay attention that the genome you used and the dbSNP file are both using the same chromosome prefix. Indeed certain genomes do not contain the chr prefix. For this reason you will need to remove the chr from your file. You can check the chromosome suffix looking at the genome index (.fai file) or at the bam headers (samtools view -H bam file).
To remove the chr from the dbSNP file you can use the command sed 's/^chr//' dbSNP.vcf > dbSNP.woChr.vcf
Try to avoid to indicate file paths using the ~ since snakemake and conda create "virtual environments" and sometimes the ~ can be miss-interpreted.
Contributors