Snakemake alignment script

Question

[Begonia_pavonina]

I have been trying to write a simple alignment pipeline with Snakemake. Unfortunately, I have a hard time understanding the error messages. In the example below, the message " 'str' object has no attribute 'name' " is a bit cryptic. Does it means that the expression {input.r1} is incorrect?

import os
import snakemake.io
import glob

    (SAMPLES,READS,) = glob_wildcards("{sample}_{read}.fastq.gz")
    READS=["1","2"]

    rule all:
        input: expand("{sample}.bam",sample=SAMPLES)

    rule bwa_map:
        input:
            ref="path/to/ref.fasta",
            r1="{sample}_1.fastq.gz",
            r2="{sample}_2.fastq.gz"

        output: "{sample}.bam"

        shell: "bwa mem {input.ref} {input.r1} {input.r2} | samtools view -Sbh - > {output}"

snakemake -n

Building DAG of jobs...
Traceback (most recent call last):
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/snakemake/__init__.py", line 701, in snakemake
    success = workflow.execute(
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/snakemake/workflow.py", line 1066, in execute
    logger.run_info("\n".join(dag.stats()))
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/snakemake/dag.py", line 2191, in stats
    yield tabulate(rows, headers="keys")
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/tabulate/__init__.py", line 2048, in tabulate
    list_of_lists, headers = _normalize_tabular_data(
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/tabulate/__init__.py", line 1471, in _normalize_tabular_data
    rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/tabulate/__init__.py", line 1471, in <lambda>
    rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/tabulate/__init__.py", line 107, in _is_separating_line
    (len(row) >= 1 and row[0] == SEPARATING_LINE)
  File "/mnt/shared/scratch/usr/apps/conda/lib/python3.8/site-packages/snakemake/rules.py", line 1138, in __eq__
    return self.name == other.name and self.output == other.output
AttributeError: 'str' object has no attribute 'name'

Answer 1

[DBScan]

Make sure you have proper indentation, when I run your code and fix the indentation it works fine.

import os
import snakemake.io
import glob

(SAMPLES,READS,) = glob_wildcards("{sample}_{read}.fastq.gz")
READS=["1","2"]

rule all:
        input: expand("{sample}.bam",sample=SAMPLES)

rule bwa_map:
        input:
                ref="path/to/ref.fasta",
                r1="{sample}_1.fastq.gz",
                r2="{sample}_2.fastq.gz"

output: "{sample}.bam"

shell: "bwa mem {input.ref} {input.r1} {input.r2} | samtools view -Sbh - > {output}"

[Begonia_pavonina]

It is working, the same error did not show up. Another error show up ("Missing input files for rule all:"), but I think it is more linked to my dataset.

I don't understand the logic of it. The output: and shell: lines are included in the rule bwa_map:, why not indenting them??

Answer 2

[dariober]

You are probably hitting this issue https://github.com/snakemake/snakemake/issues/1899. Perhaps you are using an old version of snakemake with a recent version of the tabulate module. Try upgrading to the latest snakemake and if that doesn't fix it, post some details of your snakemake version and python.

[Begonia_pavonina]

I am working with Python 3.8.12 and Snakemake 6.15.5, and try to update to 7.32.4, even though my conda/mamba is not working properly.

[Begonia_pavonina]

I have upgraded mamba and conda, then re-installed snakemake 7.32.4. It is now working well with the proper indentation.

import os
import snakemake.io
import glob

(SAMPLES,READS,) = glob_wildcards("{sample}_{read}.fastq.gz")
READS=["1","2"]

rule all:
        input: expand("{sample}.bam",sample=SAMPLES)

rule bwa_map:
        input:
                ref="path/to/ref.fasta",
                r1="{sample}_1.fastq.gz",
                r2="{sample}_2.fastq.gz"

        output: "{sample}.bam"

        shell: "bwa mem {input.ref} {input.r1} {input.r2} | samtools view -Sbh - > {output}"