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nanoporetech / pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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snakemake install failure #6

Open chansnotes opened 4 years ago

chansnotes commented 4 years ago

Hello.

I'm having trouble installing using snakemake...

Output log is shown below:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   all
    1   filter_region
    1   filter_vcf
    1   index_vcf
    1   reformat_vcf
    1   sort_vcf
    6

[Tue Nov 19 10:56:35 2019]
rule filter_region:
    input: my_sample/sv_calls/my_sample_sniffles_tmp.vcf, my_sample/target.bed, init
    output: my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf
    jobid: 10
    wildcards: sample=my_sample

bcftools view -T my_sample/target.bed my_sample/sv_calls/my_sample_sniffles_tmp.vcf -o my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf
Activating conda environment: /BiO/tutorial/pipeline-structural-variation-1.4.0/results/.snakemake/conda/0ebb204c
/bin/bash: bcftools: command not found
[Tue Nov 19 10:56:39 2019]
Error in rule filter_region:
    jobid: 10
    output: my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf
    conda-env: /BiO/tutorial/pipeline-structural-variation-1.4.0/results/.snakemake/conda/0ebb204c
    shell:
        bcftools view -T my_sample/target.bed my_sample/sv_calls/my_sample_sniffles_tmp.vcf -o my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
yeemey commented 4 years ago

(I'm not a developer on this project.) Based on this:

Activating conda environment: /BiO/tutorial/pipeline-structural-variation-1.4.0/results/.snakemake/conda/0ebb204c /bin/bash: bcftools: command not found

It looks like bcftools is either not installed, or not accessible somehow, even though I would've thought that it's included in the conda environment.

pkubioinformatics commented 4 years ago

(I'm not a developer on this project too.) try to install samtools, minimap2 by running: $ conda install samtools $ conda install minimap2 and run snakemake use 1 thread, which works for me.(I found there were 4 separated bam files in /Analysis/alignment which should be join into 1 bam file if you run snakefmake with the default 4 threads) $ snakemake --snakefile ./pipeline-structural-variation/Snakefile --configfile ./config.yaml --jobs 1 eval

good luck