我有以下zip存档结构：
$ unzip -l Undetermined_S0_L004_R1_001_fastqc.zip
Archive: Undetermined_S0_L004_R1_001_fastqc.zip
Length Date Time Name
-------- ---- ---- ----
0 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/
0 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/
0 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/
1197 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/fastqc_icon.png
1450 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/warning.png
1561 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/error.png
1715 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/tick.png
782 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/summary.txt
9095 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_base_quality.png
14381 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_tile_quality.png
23205 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_sequence_quality.png
30978 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_base_sequence_content.png
31152 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_sequence_gc_content.png
7861 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_base_n_content.png
18356 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/sequence_length_distribution.png
23040 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/duplication_levels.png
9096 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/adapter_content.png
58683 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/kmer_profiles.png
355919 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/fastqc_report.html
301092 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/fastqc_data.txt
10117 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/fastqc.fo
-------- -------
899680 21 files
怎么可能使用fastqc_data.txt与crimson并行，因为此刻我得到以下错误：
find `pwd`/*_fastqc.zip -type f | parallel -j 3 unzip -c {} {}/fastqc_data.txt | crimson fastqc {} | less
Usage: crimson fastqc [OPTIONS] INPUT [OUTPUT]
Error: Invalid value for "input": Path "{}" does not exist.
您有一个由四个命令组成的管道：
find，其中列出了zip文件。parallel，该调用unzip将在每个zip文件中提取一个文件。假设该文件{}已替换为zip文件的路径，则您尝试home/user977828/stuff/Undetermined_S0_L004_R1_001_fastqc.zip/fastqc_data.txt从存档中提取文件（如果当前目录为/home/user977828/stuff）。crimson，它接收标准输入提取的文件的混乱，并且被调用的论点fastqc和{}，less。parallel仅替换{}其参数。它对管道的其他部分无能为力。如果要分别crimson在每个fastqc_data.txt文件上调用，则需要将管道从unzip传递crimson为作为的参数parallel。
find *_fastqc.zip -type f | sed 's/\.zip$//' |
parallel -j 3 'unzip -c {}.zip {}/fastqc_data.txt | crimson fastqc /dev/stdin' |
less
本文收集自互联网，转载请注明来源。
如有侵权，请联系 [email protected] 删除。
我来说两句