Question: How can I run a same command in mac terminal for multiple files in a folder?
0
gravatar for vermaakhilkr01
3 months ago by
vermaakhilkr010 wrote:

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)

sequencing rna-seq alignment • 176 views
ADD COMMENTlink modified 3 months ago by genomax56k • written 3 months ago by vermaakhilkr010

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax56k

Mouse genome. And RAM isn't the problem. I've got a RAM 64 GB desktop(Mac, currently using) and 192 GB RAM Workstation Dell.

ADD REPLYlink written 3 months ago by vermaakhilkr010
2
gravatar for genomax
3 months ago by
genomax56k
United States
genomax56k wrote:

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/
ADD COMMENTlink modified 3 months ago • written 3 months ago by genomax56k

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

ADD REPLYlink written 3 months ago by vermaakhilkr010

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
ADD REPLYlink modified 3 months ago • written 3 months ago by genomax56k
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