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Linux에서 파이프라인 실행 [닫기]

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Linux에서 파이프라인 실행 [닫기]

이 스크립트가 있습니다

#!/bin/bash
module load bedtools/2.21.0
bamfiles=(
/temp/hgig/fi1d18/1672_WTSI-COLO_023_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_023_1pre.dupmarked.bam
/temp/hgig/fi1d18/1672_WTSI-OESO_005_w3/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_005_w3.dupmarked.bam
/temp/hgig/fi1d18/1672_WTSI-OESO_036_2post/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_036_2post.dupmarked.bam
/temp/hgig/fi1d18/1672_WTSI-COLO_021_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_021_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_027_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_027_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_011_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_011_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_176_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_176_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_170_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_170_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_141_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_141_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLIVM_005_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLIVM_005_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_099_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_099_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_085_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_085_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_075_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_075_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_027_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_027_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_021_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_021_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-OESO_036_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_036_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_005_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_005_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_023_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_023_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_121_1pre.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-OESO_013_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_013_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-OESO_005_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_005_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_011_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_011_a_RNA.dupmarked.bam 
/temp/hgig/fi1d18/1672_WTSI-COLO_019_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-COLO_019_1pre.dupmarked.bam
)

for file in "${bamfiles[@]}"; do
    fname=$(basename "$file")
    fdir=$(dirname "$file")
    bamtofastq -i "$file" -fq "${fdir}/${fname%.bam}.fq"
done

나는 이것을 실행한다

[fi1d18@cyan01 ~]$ chmod +x run.sh

[fi1d18@cyan01 ~]$ run.sh
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
basename: invalid option -- 's'
Try `basename --help' for more information.
./run.sh: line 30: bamtofastq: command not found
[fi1d18@cyan01 ~]$


[fi1d18@cyan01 ~]$ run.sh
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
./run.sh: line 32: bamtofastq: command not found
[fi1d18@cyan01 ~]$

답변1

귀하의 질문에 제한된 정보가 주어지고 귀하의 bamtofastq명령이 다음과 같다고 가정합니다.이것bedtools 패키지에서 다음을 생각해냈습니다.

#!/bin/bash

bamfiles=(
    /path/to/file1.bam
    /path/to/file2.bam
    /path/to/file3.bam
)

for file in "${bamfiles[@]}"; do
    fname=$(basename "$file")
    fdir=$(dirname "$file")
    bedtools bamtofastq -i "$file" -fq "${fdir}/${fname%.bam}.fq"
done

이는 모든 bam 파일을 스크립트에 수동으로 채우고 .fq 파일이 해당 bam 파일과 동일한 디렉터리에 있기를 원한다고 가정합니다. 그렇지 않은 경우, 귀하의 질문에 보다 효과적으로 답변할 수 있도록 추가 정보를 제공해 주십시오.

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