Calling another pipeline within a snakefile result in mising output errors

Question

I am using an assembly pipeline called Canu inside my snakemake pipeline, but when it comes to the rule calling Canu, snakemake exits witht he MissingOutputException error as the pipeline submits multiple jobs to the cluster itself so it seems snakemake expects the output after the first job has finished. Is there a way to avoid this? I know I could use a very long --latency-wait option but this is not very optimal.

snakefile code:

#!/miniconda/bin/python

workdir: config["path_to_files"]
wildcard_constraints:
    separator = config["separator"],
    sample = '|' .join(config["samples"]),

rule all:
    input:
        expand("assembly-stats/{sample}_stats.txt", sample = config["samples"])

rule short_reads_QC:
    input:
        f"short_reads/{{sample}}_short{config['separator']}*.fq.gz"

    output:
        "fastQC-reports/{sample}.html"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        """
        mkdir fastqc-reports
        fastqc -o fastqc-reports {input}
        """

rule quallity_trimming:
    input:
        forward = f"short_reads/{{sample}}_short{config['separator']}1.fq.gz",
        reverse = f"short_reads/{{sample}}_short{config['separator']}2.fq.gz",

    output:
        forward = "cleaned_short-reads/{sample}_short_1-clean.fastq",
        reverse = "cleaned_short-reads/{sample}_short_2-clean.fastq"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        "bbduk.sh -Xmx1g in1={input.forward} in2={input.reverse} out1={output.forward} out2={output.reverse}  qtrim=rl trimq=10"

rule long_read_assembly:
    input:
        "long_reads/{sample}_long.fastq.gz"

    output:
        "canu-outputs/{sample}.subreads.contigs.fasta"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        "canu -p {wildcards.sample} -d canu-outputs genomeSize=8m -pacbio-raw {input}"
rule short_read_alignment:
    input:
        short_read_fwd = "cleaned_short-reads/{sample}_short_1-clean.fastq",
        short_read_rvs = "cleaned_short-reads/{sample}_short_2-clean.fastq",
        reference = "canu-outputs/{sample}.subreads.contigs.fasta"

    output:
        "bwa-output/{sample}_short.bam"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        "bwa mem {input.reference} {input.short_read_fwd} {input.short_read_rvs} |  samtools view -S -b > {output}"


rule indexing_and_sorting:
    input:
        "bwa-output/{sample}_short.bam"
    output:
        "bwa-output/{sample}_short_sorted.bam"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        "samtools sort {input} > {output}"

rule polishing:
    input:
        bam_files = "bwa-output/{sample}_short_sorted.bam",
        long_assembly = "canu-outputs/{sample}.subreads.contigs.fasta"

    output:
        "pilon-output/{sample}-improved.fasta"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        "pilon --genome {input.long_assembly} --frags {input.bam_files} --output {output} --outdir pilon-output"

rule assembly_stats:
    input:
        "pilon-output/{sample}-improved.fasta"
    output:
        "assembly-stats/{sample}_stats.txt"

    conda:
        "/home/lamma/env-export/hybrid_assembly.yaml"

    shell:
        "stats.sh in={input} gc=assembly-stats/{wildcards.sample}/{wildcards.sample}_gc.csv gchist=assembly-stats/{wildcards.sample}/{wildcards.sample}_gchist.csv shist=assembly-stats/{wildcards.sample}/{wildcards.sample}_shist.csv > assembly-stats/{wildcards.sample}/{wildcards.sample}_stats.txt"

The exact error:

Waiting at most 60 seconds for missing files.
MissingOutputException in line 43 of /faststorage/home/lamma/scripts/hybrid_assembly/bacterial-hybrid-assembly.smk:
Missing files after 60 seconds:
canu-outputs/F19FTSEUHT1027.PSU4_ISF1A.subreads.contigs.fasta
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

The snakemake command being used:

snakemake --latency-wait 60 --rerun-incomplete --keep-going --jobs 99 --cluster-status 'python /home/lamma/faststorage/scripts/slurm-status.py' --cluster 'sbatch  -t {cluster.time} --mem={cluster.mem} --cpus-per-task={cluster.c} --error={cluster.error}  --job-name={cluster.name} --output={cluster.output}' --cluster-config bacterial-hybrid-assembly-config.json --configfile yaml-config-files/test_experiment3.yaml --use-conda --snakefile bacterial-hybrid-assembly.smk

Which cluster are you using? See this [answer](https://stackoverflow.com/a/50038772/3998252) that describes solution for your problem. Basically, add `wait` after `canu` command and add corresponding flag to cluster command to respect `wait`. — Manavalan Gajapathy, Jan 07 '20 at 15:46
I added an edit of my snakemake command to the question. The cluster I am using is Slurm based. and that you I will try use wait. — Lamma, Jan 08 '20 at 08:16

score 0 · Answer 1 · answered Jan 07 '20 at 17:11

0

I surmise that canu is giving you canu-outputs/{sample}.contigs.fasta not canu-outputs/{sample}.subreads.contigs.fasta. If so edit the canu commad to be

canu -p {wildcards.sample}.subreads ...

(By the way, I don't think #!/miniconda/bin/python is necessary).

answered Jan 07 '20 at 17:11

dariober

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the -p flag is just for a prefix as canu output about 10 files. Oh really I thought I had to direct the script to where my python is installed? – Lamma Jan 08 '20 at 08:05
@Lamma my suggestion, in fact, is that the prefix should be `{wildcards.sample}.subreads` so that in output you get `canu-outputs/{sample}.subreads.contigs.fasta`. – dariober Jan 08 '20 at 09:18
You execute the Snakefile via snakemake not directly by python. Snakemake will see `#!/miniconda...` just as a comment and ignore it. – dariober Jan 08 '20 at 09:21
subreads.contigs.fasta is a file created by canue so adding subreads to the prifix would just result in `{sample}.subreads.subreads.contigs.fasta` – Lamma Jan 08 '20 at 10:14

Calling another pipeline within a snakefile result in mising output errors

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