Closed weir12 closed 5 years ago
Hi!
You have to specify the absolute path to the files, such as:
transcriptome: "/home/weir/output/Nanopore-DEG-Analysis/Araport11_genes.201606.cdna.fasta"
Also, minimap2_opts
should be only "-uf -k14" and
minimap_index_opts
should be "-k14".
Best, Botond
Hello!
Pandas is a dependency which has to be present in the environment from which you are invoking snakemake. It is not necessary to install it in the environment created by --use-conda.
Botond
Hi Botond,
I was in a trouble when I tried to run sankefile like this:
$ snakemake --use-conda -j 4 all
Error Report:Attached my config.yml
The transcripts and annotations were downloaded from:(https://www.arabidopsis.org/) minimap2 --version :2.15-r905 snakemake was installed by conda(4.6.7). All my input files are exist in
/home/weir/output/Nanopore-DEG-Analysis/
In addition,I successfully tried manually indexing ref.fa by minimap2 command: minimap2 -d ref.mmi ref.fa