How can I run a same command in mac terminal for multiple files in a folder?

Question

[iamakhilverma]

How can I run the same command in mac terminal for multiple files in a folder? The files are named like 24538_7#1_paired1.fq, 24538_7#1_paired2.fq, 24538_7#2_paired1.fq, 24538_7#2_paired2.fq, 24538_7#3_paired1.fq, 24538_7#3_paired2.fq, and so on.

The command is:

STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#1_paired1.fq data/24538_7#1_paired2.fq --outFileNamePrefix results/STAR/

Since filename involves a counter, so, obviously the filenames need to be changed.

I was trying to write command, but it's giving segmentation fault. My effort for the command is below:

for file in 24538_7#*.fq; do STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/"${file%.fq}_paired1.fq" data/"${file%.fq}_paired2.fq" --outFileNamePrefix results/STAR/ ; done

(PS- I use MacOS)

[GenoMax]

What genome are you aligning against? STAR requires at least 30+G of free RAM (for human sized genomes) so unless you have that available that may be your first problem.

[iamakhilverma]

Mouse genome. RAM isn't an issue for me. I've got a RAM 64 GB desktop(Mac- currently in use) and a 192 GB RAM Workstation Dell (in-store).

Answer 1

[GenoMax]

This looks correct. Remove the word echo when ready to run.

for file in 24538_7#*paired1.fq; do echo STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/"${file%%_paired1.fq}_paired1.fq" data/"${file%%_paired1.fq}_paired2.fq" --outFileNamePrefix results/STAR/ ; done
STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#1_paired1.fq data/24538_7#1_paired2.fq --outFileNamePrefix results/STAR/
STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#2_paired1.fq data/24538_7#2_paired2.fq --outFileNamePrefix results/STAR/
STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#3_paired1.fq data/24538_7#3_paired2.fq --outFileNamePrefix results/STAR/

[iamakhilverma]

It's creating only 1 output file. (actually, it's rewriting the same output file for every input file)

[GenoMax]

For an idea of how you can get unique names for the output. Modify the last part as needed.

for file in 24538_7#*paired1.fq; do echo STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/"${file%%_paired1.fq}_paired1.fq" data/"${file%%_paired1.fq}_paired2.fq" --outFileNamePrefix results/STAR/${file%%_paired1.fq}.STAR ; done
STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#1_paired1.fq data/24538_7#1_paired2.fq --outFileNamePrefix results/STAR/24538_7#1.STAR
STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#2_paired1.fq data/24538_7#2_paired2.fq --outFileNamePrefix results/STAR/24538_7#2.STAR
STAR --runThreadN 12 --genomeDir indices/STAR --twopassMode Basic --readFilesIn data/24538_7#3_paired1.fq data/24538_7#3_paired2.fq --outFileNamePrefix results/STAR/24538_7#3.STAR