Snakemake is a workflow management system with a Python-style specification language.
Snakemake is a workflow management system with a Python-style specification language.
Questions tagged [snakemake]
1634 questions
0
votes
1 answer
the jobs option does not define the number of submited jobs
The command that I use to trigger snakemake is:
snakemake --snakefile Snakefile --configfile config.json --latency-wait 60 --rerun-incomplete --keep-going --notemp --reason --use-singularity --singularity-args "--bind /somepath/folder" --jobs 400…
nicoluca
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- 7
0
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1 answer
Snakemake “Missing files after X seconds” error
I am getting the following error every time I try to run my snakemake script:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 99
Job counts:
count jobs
1 all
1 antiSMASH
1 …
Lamma
- 895
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1 answer
"one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode", I am not sure why I am getting this error
I am getting the following error:
one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!
My snakefile looks like the following:
#!/miniconda/bin/python
workdir: config["path_to_files"]
wildcard_constraints:
…
Lamma
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0
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1 answer
Snakemake "Missing files after X seconds" error
I am getting the following error every time I try to run my snakemake script:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 …
Lamma
- 895
- 1
- 12
- 26
0
votes
2 answers
Snakemake merge multiples bam files using bamtools
I have several BAM files in different directories that I want to merge. In my config.yaml file I indicate the paths to the files I want to merge:
var:
var1: [ "/DATA/utent3/DATI/var/var1/leaf/trimmed/leaf_var1_ref1.bam",…
user3224522
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1 answer
A question about parallelization overhead and I/O bound rules
Imagine the following snakefile adapted (in the end of this post) from Handling parallelization
and the rule MY_RULE is I/O bound (let's say that I need to load a very heavy model to apply this rule into a file).
With the way wildcards are used in…
Tiago Freitas Pereira
- 690
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1 answer
How to assign multiple paths from the config.yaml?
I would like to use snakemake to analyze my data sets. As I am going to work with different organisms, I would like snakemake to create a folder for each of them when indexing the genome.
I have created the following structure in my config…
Assa Yeroslaviz
- 590
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0
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2 answers
snakemake: pipeline failed with MissingOutputException
To make it clear I have to modify the post. The situation is that at the beginning I ran the pipeline well on a local machine but failed when submitted to cluster. After posting the question, I found the version of snakemake was 3.13.3, so I updated…
Dianyu Chen
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- 2
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1 answer
mapping reads using snakemake
I am trying to run hisat2 mapping using the snakemake.
Basically, I'm using a config.yaml file like this:
reads:
set1: /path/to/set1/samplelist.tab
hisat2:
database: genome
genome: genome.fa
nodes: 2
memory: 8G
arguments:…
user3224522
- 1,119
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- 19
0
votes
1 answer
snakemake log files for failed jobs on slurm don't exist
I am running a snakemake pipeline on a slurm HPC. Occasionally, jobs will fail due to exceeded wall time or memory. Such failed jobs do not create log files, or their log files are deleted as part of snakemakes automatic removal of files associated…
Manninm
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0
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2 answers
Altering snakemake workflow to anticipate and accommodate different data-structures
I have an existing snakemake RNAseq workflow that works fine with a directory tree as below. I need to alter the workflow so that it can accommodate another layer of directories. Currently, I use a python script that os.walks the parent directory…
Manninm
- 151
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- 7
0
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1 answer
Snakemake tabular configuration, expand, and merge - how to expand input files correctly?
I would greatly appreciate a little pointer for the following. I have a TSV samples table:
Sample Unit Tumor_or_Normal Fastq1 Fastq2
A 1 T reads/a.t.1.fastq reads/a.t.2.fastq
A 2 N reads/a.n.1.fastq …
Toshiro K. Ohsumi
- 133
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0
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1 answer
snakemake: missing last rule by changing rull all command lines
below is my snakemake codes, if i don't comment out line28,29 code,which is rule all->input->the 1st,2nd command lines,then I can't get the last rule varscan_somatic, that is to say,the dry run output likes this:
Job counts:
count jobs
…
Danielle
- 19
- 5
0
votes
1 answer
Snakemake expand and zip working together to produce unexpected wildards
Trying to use expand and zip properly to expand two lists for defining the output rule is leading to new wildcards that I didn't think would be defined
BASES = ['wt_base', 'wt', 'wt_base_ars', 'F210i_base', 'no_4su']
CONTRASTS = ['f210i_base',…
Al Bro
- 383
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0
votes
1 answer
Snakemake - how do I input a range of different files delineated from each other numerically?
This seems like a basic question but I keep getting some variation of the error: No values given for wildcard.
I have a group of 22 files named Ne-sQTL_perind.counts.gz.qqnorm_chr{#}.gz. I would like to act on them in a rule. What I have originally…
CelineDion
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