Only makes minimap2 index and then finishes

[callumparr]

I edited config.yml and ran on input of a ~40,000 reads (originally 100,000 before pychopper) for a test. However it only seems to make the config.pdf

`tm1612s-MacBook-Pro:pipeline-pinfish-analysis callum$ snakemake --use-conda -j all Building DAG of jobs... Creating conda environment /Users/callum/pipeline-pinfish-analysis/env.yml... Downloading remote packages. Environment for ../../../../env.yml created (location: .snakemake/conda/ba04bccc) Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Job counts: count jobs 1 build_minimap_index 1

[Thu Jan 31 00:54:03 2019] rule build_minimap_index: input: /Users/callum/Genome_files/hg38.fa output: index/genome_index.mmi jobid: 0 threads: 2

Activating conda environment: /Users/callum/pipeline-pinfish-analysis/Users/callum/Sync_later/pipeline-pinfish-analysis_HDF/.snakemake/conda/ba04bccc [M::mm_idx_gen::86.9001.60] collected minimizers [M::mm_idx_gen::116.8361.66] sorted minimizers [M::main::140.9161.53] loaded/built the index for 455 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 455 [M::mm_idx_stat::142.3351.52] distinct minimizers: 100202295 (37.96% are singletons); average occurrences: 5.732; average spacing: 5.587 [M::main] Version: 2.15-r905 [M::main] CMD: minimap2 -t 2 -k15 -I 1000G -d index/genome_index.mmi /Users/callum/Genome_files/hg38.fa [M::main] Real time: 143.857 sec; CPU: 218.279 sec; Peak RSS: 7.965 GB [Thu Jan 31 00:56:27 2019] Finished job 0. 1 of 1 steps (100%) done Complete log: /Users/callum/pipeline-pinfish-analysis/.snakemake/log/2019-01-31T005121.607446.snakemake.log`

I can confirm index mmi file was outputted to working directory given. I attach config.yml file in case there is some issue that it doesn't proceed with next steps?

[bsipos]

Hi,

I think it should be snakemake --use-conda -j 50 all, where 50 is the number of threads.

Botond

[callumparr]

oh yes thats very true. thats embarrassing. Thank you.