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(Terminal) How to loop through files while still multithreading?

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0

I am running a (bioinformatics) package called fastqc. The command I'm running allows users to specify the number of threads to use. For example:

patrick$ fastqc 039210Sm_S1_L001_R1_001.fastq.gz 039210Sm_S1_L001_R2_001.fastq.gz --extract --outdir=/the/output/folder --threads=2

will execute the command on both files at once, as desired. In practice, I cannot copy-paste the names of each file (since there aren't just two, but rather 100s). So instead what I am trying to do is change my directory to the folder where these documents are stored and run code that will loop through each file. This is what I came up with:

patrick$ cd folder/containing/my/files
patrick$ for i in *.fastq.gz; 
>do fastqc $i --extract --outdir=/the/output/folder --threads=4;
>done

However, this code does not run on four files at once. Rather, it only uses one thread. Is there any way to loop through every file in a folder while still multithreading?
One thing I thought about was exporting all the file names to a text document via ls > names.txt, but I wasn't sure how to proceed from there, nor was I able to find anyone on the forums with an analogous problem.

Thank you for taking the time to read this, regardless of whether or not you knew the answer.

OS information: I am using Terminal version 2.9.1 (421.1) on a MacBook Pro (Retina, 15-inch, Mid 2015).

Temporary workaround: I ran ls > names.txt, opened that file in Word, found all enters ^p and replaced it with a space, . Copied and pasted that entire document into Terminal. That one command took up 25 lines and the whole process takes a while, but other than that it's working alright. Still looking for a solution, though.

multithreading terminal

share|improve this question

edited Mar 8 at 3:57

Patrick

asked Mar 7 at 6:06

PatrickPatrick

63

add a comment | 

0

I am running a (bioinformatics) package called fastqc. The command I'm running allows users to specify the number of threads to use. For example:

patrick$ fastqc 039210Sm_S1_L001_R1_001.fastq.gz 039210Sm_S1_L001_R2_001.fastq.gz --extract --outdir=/the/output/folder --threads=2

will execute the command on both files at once, as desired. In practice, I cannot copy-paste the names of each file (since there aren't just two, but rather 100s). So instead what I am trying to do is change my directory to the folder where these documents are stored and run code that will loop through each file. This is what I came up with:

patrick$ cd folder/containing/my/files
patrick$ for i in *.fastq.gz; 
>do fastqc $i --extract --outdir=/the/output/folder --threads=4;
>done

However, this code does not run on four files at once. Rather, it only uses one thread. Is there any way to loop through every file in a folder while still multithreading?
One thing I thought about was exporting all the file names to a text document via ls > names.txt, but I wasn't sure how to proceed from there, nor was I able to find anyone on the forums with an analogous problem.

Thank you for taking the time to read this, regardless of whether or not you knew the answer.

OS information: I am using Terminal version 2.9.1 (421.1) on a MacBook Pro (Retina, 15-inch, Mid 2015).

Temporary workaround: I ran ls > names.txt, opened that file in Word, found all enters ^p and replaced it with a space, . Copied and pasted that entire document into Terminal. That one command took up 25 lines and the whole process takes a while, but other than that it's working alright. Still looking for a solution, though.

multithreading terminal

share|improve this question

edited Mar 8 at 3:57

Patrick

asked Mar 7 at 6:06

PatrickPatrick

63

add a comment | 

I am running a (bioinformatics) package called fastqc. The command I'm running allows users to specify the number of threads to use. For example:

patrick$ fastqc 039210Sm_S1_L001_R1_001.fastq.gz 039210Sm_S1_L001_R2_001.fastq.gz --extract --outdir=/the/output/folder --threads=2

will execute the command on both files at once, as desired. In practice, I cannot copy-paste the names of each file (since there aren't just two, but rather 100s). So instead what I am trying to do is change my directory to the folder where these documents are stored and run code that will loop through each file. This is what I came up with:

patrick$ cd folder/containing/my/files
patrick$ for i in *.fastq.gz; 
>do fastqc $i --extract --outdir=/the/output/folder --threads=4;
>done

However, this code does not run on four files at once. Rather, it only uses one thread. Is there any way to loop through every file in a folder while still multithreading?
One thing I thought about was exporting all the file names to a text document via ls > names.txt, but I wasn't sure how to proceed from there, nor was I able to find anyone on the forums with an analogous problem.

Thank you for taking the time to read this, regardless of whether or not you knew the answer.

OS information: I am using Terminal version 2.9.1 (421.1) on a MacBook Pro (Retina, 15-inch, Mid 2015).

Temporary workaround: I ran ls > names.txt, opened that file in Word, found all enters ^p and replaced it with a space, . Copied and pasted that entire document into Terminal. That one command took up 25 lines and the whole process takes a while, but other than that it's working alright. Still looking for a solution, though.

multithreading terminal

share|improve this question

edited Mar 8 at 3:57

Patrick

asked Mar 7 at 6:06

PatrickPatrick

63

patrick$ fastqc 039210Sm_S1_L001_R1_001.fastq.gz 039210Sm_S1_L001_R2_001.fastq.gz --extract --outdir=/the/output/folder --threads=2

patrick$ cd folder/containing/my/files
patrick$ for i in *.fastq.gz; 
>do fastqc $i --extract --outdir=/the/output/folder --threads=4;
>done

share|improve this question

edited Mar 8 at 3:57

Patrick

asked Mar 7 at 6:06

PatrickPatrick

63

share|improve this question

edited Mar 8 at 3:57

Patrick

asked Mar 7 at 6:06

PatrickPatrick

63

asked Mar 7 at 6:06

PatrickPatrick

63

asked Mar 7 at 6:06

PatrickPatrick

63