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2 hours ago by

University of California, Davis

I am using Snakemake to build my pipeline. Here is the code in Snakefile.

rule all:
    input: 
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.1.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.2.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.3.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.4.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.rev1.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.rev2.bt2",

rule download_genome:
    output:
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz"
    shell:
        "wget ftp://ftp.ensemblgenomes.org/pub/fungi/release-49/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz -O {output}"

rule unzip_genome:
    input:
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz"    
    output:
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa"
    shell:
        "gunzip {input}"
rule build_index:
    input:
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa"
    params:
        basename="bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel"
    conda:
        "env/environment.yaml"
    output:
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.1.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.2.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.3.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.4.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.rev1.bt2",
        "bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.rev2.bt2",
    shell:
        "bowtie2-build {input} {params.basename}"

Running snakemake using following command:

snakemake --latency-wait 60 --use-conda --core 1

Which is giving following error:

Waiting at most 60 seconds for missing files.
MissingOutputException in line 25 of /Users/biplab/Documents/chip_seq_pipeline/Snakefile:
Job Missing files after 60 seconds:
bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.rev1.bt2
bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.rev2.bt2
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. completed successfully, but some output files are missing. 3
  File "/Users/biplab/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 575, in handle_job_success
  File "/Users/biplab/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 247, in handle_job_success
Removing output files of failed job build_index since they might be corrupted:
bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.1.bt2, bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.2.bt2, bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.3.bt2, bowtie_index/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.4.bt2
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /Users/biplab/Documents/chip_seq_pipeline/.snakemake/log/2020-12-12T132821.191011.snakemake.log

I am not sure what is wrong with this code. It will be great is anyone can help me with this error. Thank you so much.

Biplab

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modified 1 hour ago

written
2 hours ago
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biplab110



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