MissinOutputException在snakemake

Question

我計劃我的生物信息學管道進入snakemake因爲我目前的管道是多個腳本越來越難追的集合。在教程和文檔的基礎上，snakemake似乎是流水線管理非常明確和有趣的選擇。但是，我不熟悉Python，因爲我主要是使用bash和R工作，所以snakemake似乎有點難以學習：我現在面臨以下問題。

我有兩個文件，sampleA_L001_R1_001.fastq.gz和sampleA_L001_R2_001.fastq.gz，wchich被放置到同一個目錄sampleA。我想通過使用cat命令來合併這些文件。這實際上是一個測試運行：在實際情況下，我會爲每個樣本使用八個單獨的FASTQ文件，這些文件應以類似的方式合併。非常簡單的工作，但我的代碼有問題。

snakemake --latency-wait 20 --snakefile /home/users/me/bin/snakefile.txt 

rule mergeFastq: 
    input: 
     reads1='sampleA/sampleA_L001_R1_001.fastq.gz', 
     reads2='sampleA/sampleA_L001_R2_001.fastq.gz' 
    output: 
     reads1='sampleA/sampleA_R1.fastq.gz', 
     reads2='sampleA/sampleA_R2.fastq.gz' 
    message: 
     'Merging FASTQ files...' 
    shell: 
     'cat {input.reads1} > {output.reads1}' 
     'cat {input.reads2} > {output.reads2}' 

------------------------------------------------------------- 

Provided cores: 1 
Rules claiming more threads will be scaled down. 
Job counts: 
    count jobs 
    1 mergeFastq 
    1 

Job 0: Merging FASTQ files... 

Waiting at most 20 seconds for missing files. 
Error in job mergeFastq while creating output files sampleA_R1.fastq.gz, sampleA_R2.fastq.gz. 
MissingOutputException in line 5 of /home/users/me/bin/snakefile.txt: 
Missing files after 20 seconds: 
sampleA_R1.fastq.gz 
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. 
Removing output files of failed job mergeFastq since they might be corrupted: sampleA_R2.fastq.gz 
Will exit after finishing currently running jobs. 
Exiting because a job execution failed. Look above for error message. 

正如你所看到的，我已經嘗試過--latency-wait選項沒有任何成功。你有什麼想法可能是我的問題的根源？文件路徑是正確的，文件本身沒有損壞，並確定。我也遇到了與通配符類似的問題，所以在snakemake基礎知識中一定有一些我不明白的地方。

Answer 1

的問題是在Shell語句，它被連接成一個命令，它生成一個文件「sampleA/sampleA_R1.fastq.gzcat」，這就是爲什麼snakemake沒有找到正確的輸出。例如，您可以使用以下語法：

rule mergeFastq: 
    input: 
     reads1='sampleA/sampleA_L001_R1_001.fastq.gz', 
     reads2='sampleA/sampleA_L001_R2_001.fastq.gz' 
    output: 
     reads1='sampleA/sampleA_R1.fastq.gz', 
     reads2='sampleA/sampleA_R2.fastq.gz' 
    message: 
     'Merging FASTQ files...' 
    shell:""" 
     cat {input.reads1} > {output.reads1} 
     cat {input.reads2} > {output.reads2} 
    """ 

不需要選項latency-wait。