snakemake fasterq-dump包装器属性：＆＃x27;通配符＆＃x27;对象没有属性＆＃x27; compersion＆＃x27;

Question

我正在尝试使用在我的snakemake工作流中，以下载配对 - 端fastq.gz文件。这是我的蛇：

# read a .txt file including many SRR* accession number
import pandas as pd
df = pd.read_csv('SraRunTable.txt', sep=',', header=0)

# append all accession number to a list
SAMPLES = []

for i in df['Run']:
    SAMPLES.append(i)

# snakemake workflow starts here
rule all:
    input:
        expand("/data/fastq/{sample}_1.fastq.gz", sample=SAMPLES)

rule get_fastq_pe_gz:
    output:
        # the wildcard name must be accession
        "/data/fastq/{sample}_1.fastq.gz",
        "/data/fastq/{sample}_2.fastq.gz",
    log:
        "/data/logs/{sample}.log"
    params:
        extra="--skip-technical"
    threads: 20
    wrapper:
        "v1.7.0/bio/sra-tools/fasterq-dump"

使用conda执行它后，snakemake -s fasterq-dump.snake-snake-cores 20 - use-conda，我收到了一个属性，我无法弄清楚。任何建议或解决方案都值得赞赏！

这是完整日志，包括错误消息：

Building DAG of jobs...
Creating conda environment https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/sra-tools/fasterq-dump/environment.yaml...
Downloading and installing remote packages.
Environment for https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/sra-tools/fasterq-dump/environment.yaml created (location: .snakemake/conda/fab035359fa42a09dfad78160e9b8543)
Using shell: /usr/bin/bash
Provided cores: 20
Rules claiming more threads will be scaled down.
Job stats:
job                count    min threads    max threads
---------------  -------  -------------  -------------
all                    1              1              1
get_fastq_pe_gz      422             20             20
total                423              1             20

Select jobs to execute...

[Wed Jun 15 17:10:30 2022]
rule get_fastq_pe_gz:
    output: /data/scratch/yaochung/Khrameeva/fastq/SRR8750458_1.fastq.gz, /data/scratch/yaochung/Khrameeva/fastq/SRR8750458_2.fastq.gz
    log: /data/scratch/yaochung/Khrameeva/logs/SRR8750458.log
    jobid: 62
    reason: Missing output files: /data/scratch/yaochung/Khrameeva/fastq/SRR8750458_1.fastq.gz
    wildcards: sample=SRR8750458
    threads: 20
    resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/fab035359fa42a09dfad78160e9b8543
Activating conda environment: .snakemake/conda/fab035359fa42a09dfad78160e9b8543
Traceback (most recent call last):
  File "/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/scripts/tmp4ip6wnot.wrapper.py", line 45, in <module>
    shell(
  File "/home/yaochung41/anaconda3/envs/snakemake/lib/python3.10/site-packages/snakemake/shell.py", line 139, in __new__
    cmd = format(cmd, *args, stepout=2, **kwargs)
  File "/home/yaochung41/anaconda3/envs/snakemake/lib/python3.10/site-packages/snakemake/utils.py", line 430, in format
    return fmt.format(_pattern, *args, **variables)
  File "/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/conda/fab035359fa42a09dfad78160e9b8543/lib/python3.10/string.py", line 161, in format
    return self.vformat(format_string, args, kwargs)
  File "/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/conda/fab035359fa42a09dfad78160e9b8543/lib/python3.10/string.py", line 165, in vformat
    result, _ = self._vformat(format_string, args, kwargs, used_args, 2)
  File "/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/conda/fab035359fa42a09dfad78160e9b8543/lib/python3.10/string.py", line 205, in _vformat
    obj, arg_used = self.get_field(field_name, args, kwargs)
  File "/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/conda/fab035359fa42a09dfad78160e9b8543/lib/python3.10/string.py", line 276, in get_field
    obj = getattr(obj, i)
AttributeError: 'Wildcards' object has no attribute 'accession'
[Wed Jun 15 17:10:34 2022]
Error in rule get_fastq_pe_gz:
    jobid: 62
    output: /data/scratch/yaochung/Khrameeva/fastq/SRR8750458_1.fastq.gz, /data/scratch/yaochung/Khrameeva/fastq/SRR8750458_2.fastq.gz
    log: /data/scratch/yaochung/Khrameeva/logs/SRR8750458.log (check log file(s) for error message)
    conda-env: /data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/conda/fab035359fa42a09dfad78160e9b8543

RuleException:
CalledProcessError in line 25 of /data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/fasterq-dump.snake:
Command 'source /home/yaochung41/anaconda3/bin/activate '/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/conda/fab035359fa42a09dfad78160e9b8543'; set -euo pipefail;  python /data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/.snakemake/scripts/tmp4ip6wnot.wrapper.py' returned non-zero exit status 1.
  File "/data/scratch/yaochung/TEKRABber_thesis/pipelines/fasterq-dump/fasterq-dump.snake", line 25, in __rule_get_fastq_pe_gz
  File "/home/yaochung41/anaconda3/envs/snakemake/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-06-15T170843.109776.snakemake.log

Answer 1

如果您查看 shell命令期望文件使用通配符 而不是示例，如您的规则所示。您应该能够将样本重命名为在文件名中的登录并使其起作用。