missing motus.remove.padded.sh file in conda for v3.0.3

[psecekartal]

Hello, when I install motus v3.0.3 via conda, motus.remove.padded.sh doesnt exist and I get the following error. I check the git and the file is there, maybe an issue for conda enviroments?

'.../workflow/.snakemake/conda/7382cb7a2e5c3dcc34de3695c892086f_/lib/python3.9/site-packages/motus/motus.remove.padded.sh No such file or directory\n'

Do you have any suggestion how to fix this issue? I dont want to add this file manually.

[AlessioMilanese]

Hi Ece,

It seems to me that it was not installed properly. I would try to re-install. Is the error when using snakemake? Did you try to run the tool outside of snakemake?

[psecekartal]

Hi Alessio, I installed it via snakemake and it should be normally ok. I removed the env and then forced snakemake to reinstall but the error remained. I will install outside snakemake and let you know. So far when I copy motus.remove.padded.sh to conda env for snakemake, everything works.

[psecekartal]

When I install locally, I also get same error Error: metaSNVRMPadded finished with an error Error: b'bash: /Users/ecekartal/opt/miniconda3/envs/motus/lib/python3.8/site-packages/motus/motus.remove.padded.sh: No such file or directory\n' Error: b''

[AlessioMilanese]

The file is needed for metaSNV. And I guess you are also trying to run the metaSNV commands (map_snv or snv_call)?

Can you send us the code that you use to install and run? So that we can try to reproduce the error.

[psecekartal]

I use a yaml file for motus v3.0.3, both on the server and my local machine, this file is missing. Funny enough for v3.0.1 it is there. So far I copied the file manually and it works in that case.

How I installed motus locally: conda install -c bioconda motus

Here is the .yaml file and how I run:

name: motus
channels:
  - conda-forge
  - bioconda
  - defaults
  - nodefaults
dependencies:
  - motus=3.0.3

and for running:

rule motus_map_snv:
    input:
        fastq1 = rules.samtools_fastq_separate.output.hostremoved1,
        fastq2 = rules.samtools_fastq_separate.output.hostremoved2,
    output:
        bam    = dir_output + "/motus_v3.0.3/snv/bam/{sample}.bam",
    log:
        dir_output + "/logs/motus_v3.0.3/{sample}.motus_v3_map_snv.log"
    message:
        "Running motus map snv for sample {wildcards.sample}"
    params:
        DBLoc = dir_input + "/db_mOTU"
    threads: 
        nThreads
    conda: 
       "envs/motus.yaml"
    shell:
        """
        # Generating single nucleotide variant (SNV) profiles using MGs
        # map_snv takes one or multiple sequencing files and aligns reads against the mOTU profiler database:
        motus map_snv \
            -f {input.fastq1} \
            -r {input.fastq2} \
            -l 75 \
            -t {threads} \
            -o {output.bam} \
            -db {params.DBLoc} &> {log} 
        """

rule motus_snv_call:
    input: 
        allbam    = expand('{dir}/motus_v3.0.3/snv/bam/{sample}.bam', 
        dir = dir_output, sample = allSamplesUnique)
    output:
        motus_snv = directory(dir_output + "/motus_v3.0.3/snv/motus_snv")
    log:
        dir_output + "/logs/motus_v3.0.3/motus_v3_snv_call.log"
    message:
        "Running motus merge snv for samples"
    params:
        # -d Call metaSNV on all bam files in the directory. [Mandatory]
        bam       = dir_output + "/motus_v3.0.3/snv/bam",
        DBLoc = dir_input + "/db_mOTU"
    threads: 
        nThreads
    conda: 
       "envs/motus.yaml"
    shell:
        """
        # snv_call calls variants using the metaSNV package
        motus snv_call \
            -d {params.bam} \
            -db {params.DBLoc} \
            -o {output.motus_snv} 
        """

I can share the env files via email Thank you Alessio!

[hjruscheweyh]

Hello @psecekartal. Is this issue resolved?