while read loop shell command
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0
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8.0 years ago
juncheng ▴ 200

I'm writing a shell script for alignment.

Where sample ID stored in SampleID.txt, for this I use a example SRR534526, fastq file names are SRR534526_1.fastq.gz SRR534526_2.fastq.gz

My command:

while read -r line; 
  do name=$line; 
  # Rum alignment using STAR, this gives SAM file
  /software/STAR/STAR_2.3.1z12/STAR --genomeDir ~/Homo_sapiens_assembly19_STAR/ --readFilesIn $name_1.fastq.gz $name_2.fastq.gz --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix $name
  cd ..
done < 'SampleID.txt'

Error report: gzip: .fastq.gz: No such file or directory

Apparently, the problem is $name_1.fastq.gz is not recognized as SRR534526_1.fastq.gz

Could anyone help? Thanks.

bash • 3.2k views
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8.0 years ago
Vivek ★ 2.6k

Try using quotes for _1.fastq.gz like $sample"_1.fastq.gz"

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Thanks, seams working!

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3
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8.0 years ago
Ram 36k

It's a good practice to always enclose bash variables within {}, like, in your case, ${name}_1.fastq.gz

By following this, you make it explicit which part of your string is a variable name and which part is the actual literal string.

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Thanks, you both gave good suggestions.

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