#!/bin/bash
./bbmap.sh ref=ref.fa # creating index file from the input
for $i in {ls*.fastq} # trying to run batch processing
do
./bbmap.sh in=$i out={.}
done
それは言う:
BBMap version 35.74
Retaining first best site only for ambiguous mappings.
No output file.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 3.390 seconds.
Loading index for chunk 1-2, build 1
Generated Index: 1.011 seconds.
No reads to process; quitting.
Total time: 4.443 seconds.
TestScript.sh: line 6: `$i': not a valid identifier
答え1
コマンドラインに渡し、などを使用してスクリプトから$1
参照します。$2
答え2
for $i in {ls*.fastq} # trying to run batch processing
ループを宣言するときにbashを使用すると、以前for i in {ls*.fastq} # trying to run batch processing
に値を割り当てなかったため、スペースに置き換えられるため、に変更する必要があります。$i
$i