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