Medhat
Currently, Princess works on diploid genome, so I am assuming that your sample is diploid.
Thank you for reaching, sorry for missing that in the document. I will update it. In the config.yaml file under this section: ``` # Update SNPs ############# update_snps: False paternal_snps:...
Thank you, Which conda and snakemake version you are using? What is your cluster? Do not forget you need to decide which cluster you are using in this file `princess/cluster/key_mapping.yaml`...
Thank you, The issue is `-e` is a flag. So, we need to change the command to: `./princess all -d /path/to/output/ -r ccs -e -a ngmlr -s /path/to/sample.fastq.gz -f hg38.fa...
Hi, Can you please share the error log available here: ` /mnt/chsrhome/bwu3/test_file/analysis/align/minimap/merge.log` Thanks, Medhat
Hmm, do you see a file contains the `3999` prefix from the job cluster_jobid? It could be in the directory called analysis or in a subdirectory called snake_log
So, I gave the merging these parameters: ``` time: "24:00:00" nCPUs: "8" mem: 50G ``` As you can see here `https://github.com/MeHelmy/princess/blob/master/cluster/cluster_config.yaml` Princess if the previous configuration is not found it...
Hi, in the installation script. I install the required `pypy` and export it. Like here: ``` cd $clair_dir wget https://github.com/squeaky-pl/portable-pypy/releases/download/pypy3.6-7.2.0/pypy3.6-7.2.0-linux_x86_64-portable.tar.bz2 mv pypy* pypy.tar.bz2 tar -xvjf pypy.tar.bz2 mv pypy3.* pypy #...
Can you please try to use the full path to the installation? E.g., if the installation in `~/home/source/princess`, use: `~/home/source/princess/princess -h` Thanks