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Questions tagged [snakemake]

Snakemake is a workflow management system with a Python-style specification language.

Snakemake is a workflow management system with a Python-style specification language.

1634 questions
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Using directory as input in snakemake for particulars scripts

i'm sorry if my question may seem a bit dumb. So, i'm currently trying to write a workflow on snakemake (my first, as a trainee), i've to automate a couple of steps, those steps dependings all on python scripts already made. My trouble is that the…
Debbah N
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Snakemake slurm ouput file redirect to new directory

I'm putting together a snakemake slurm workflow and am having trouble with my working directory becoming cluttered with slurm output files. I would like my workflow to, at a minimum, direct these files to a 'slurm' directory inside my working…
Ensa
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R Draws Plots with Rectangles Instead of Text

I'm building a pipeline with snakemake and using conda and singularity environments to ensure reproducibility. I run into an error where the text on my plots is replaced by rectangles After experimenting with the pipeline on Linux and Mac systems…
Tomas Bencomo
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How to immediately submit all Snakemake jobs to slurm cluster

I'm using snakemake to build a variant calling pipeline that can be run on a SLURM cluster. The cluster has login nodes and compute nodes. Any real computing should be done on the compute nodes in the form of an srun or sbatch job. Jobs are limited…
Tomas Bencomo
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snakemake cluster script ImportError snakemake.utils

I have a strange issue that comes and goes randomly and I really can't figure out when and why. I am running a snakemake pipeline like this: conda activate $myEnv snakemake -s $snakefile --configfile test.conf.yml --cluster "python $qsub_script"…
soungalo
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Using Snakemake with sun grid engine array jobs

I was wondering if anybody knew how to correctly use snakemake in a sun grid engine computing context - I'm using a shared HPC cluster and am running many jobs concurrently, but it's a large strain on the scheduler to queue up thousands of nearly…
noam
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Activating existing conda enviornments in snakemake

How do I get snakemake to activate a conda environment that already exists in my environment list? I know you can use the --use-conda with a .yaml environment file but that seems to generate a new environment which is just annoying when the…
Lamma
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sbatch: error: Batch job submission failed: Socket timed out on send/recv operation when running Snakemake

I am running a snakemake pipeline on a HPC that uses slurm. The pipeline is rather long, consisting of ~22 steps. Periodically, snakemake will encounted a problem when attempting to submit a job. This reults in the error sbatch: error: Batch job…
Manninm
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Snakemake --forceall --dag results in mysterius Error: : syntax error in line 1 near 'File' from Graphvis

My attempts to construct DAG or rulegraph from RNA-seq pipeline using snakemake results in error message from graphviz. 'Error: : syntax error in line 1 near 'File'. The error can be corrected by commenting out two print commands with no visible…
Manninm
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How to fix this "IndexError: list index out of range" in snakemake

I am setting up a new snakemake pipeline for the first time and running into an issue with the code. I have tried to make it really simple in the beginning. configfile: "config.yaml" SAMPLES, =…
rdavis
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Snakemake processing large workflow slow due to lengthy sequential checking of job completion? >100x speed reduction

I am working on a rather complex snakemake workflow that spawns several hundreds of thousands of jobs. Everything works... The workflow executes, DAG gets created (thanks to the new checkpoint implementation), but is unbearably slow. I think the…
John van Dam
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How can I globally set stderr and stdout redirection into log files in Snakemake?

I am using snakemake to build a workflow. I want that stderr and stdout of all rules are by default redirected into files logs/{rule}/{wildcards}.o and logs/{rule}/{wildcards}.e, respectively. How can I achieve this? The following code does what I…
feilchenfeldt
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snakemake define folder as output

I try to run prokka using snakemake and rule all. In the latter I define all output folders which will be produced by prokka to write the results. Prokka requires a folder to be supplied as an output rather than a file. A simplified version of what…
Feliks
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Snakemake: How to dynamically set memory resource based on input file size

I'm trying to base my cluster memory allocation for a given rule on the file size of an input file. Is this possible in snakemake and if so how? So far I have tried specifying it in the resource: section like so: rule compute2: input:…
KBoehme
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Snakemake: I keep getting The 'conda' command is not available in $PATH. when running on SGE cluster

I'm tearing my hair out here, hopefully someone can help me. Running snakemake 4.8.0 I have a snakemake pipeline, which I run with two conda envs and --use-conda and it works fine when run as a standalone pipeline. However, when I run on our…
Mick Watson
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