guzip paired fast.gz files

Kaskere · 09-01-2020, 02:27 AM

Hello,
I have a bunch of paired fastq.gz files, and I need to decompress them for further low quality data trimming.
However gunzip command is not working on paired files. Any suggestions?

this is the error output
gzip: file.fastq.gz: unexpected end of file

Thank you!

GenoMax · 09-01-2020, 03:51 AM

Are you sure the files are gzipped (is spite of what the extension says)? What does

Code:

 file one_file.fastq.gz

say?

Kaskere · 09-01-2020, 04:52 AM

Quote:

Originally Posted by GenoMax

Are you sure the files are gzipped (is spite of what the extension says)? What does

Code:

 file one_file.fastq.gz

say?

myfile.fastq.gz: gzip compressed data, from FAT filesystem (MS-DOS, OS/2, NT)

they are compressed..

These paired end files were obtained after PE Trimmomatics

Biocomputronics · 09-01-2020, 09:17 AM

Try using "zcat" to see if it can display the file contents like:

zcat file.fastq.gz

If it displays the file contents, then redirect the output to a new file like:

zcat file.fastq.gz > new_file.fastq

GenoMax · 09-01-2020, 10:58 AM

@kaskere: Were these files compressed using Windows zip program? You may need to use "-S .zip" option for gunzip.

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09-01-2020, 02:27 AM	#1
Kaskere Junior Member Location: Europe Join Date: Jul 2018 Posts: 6	guzip paired fast.gz files Hello, I have a bunch of paired fastq.gz files, and I need to decompress them for further low quality data trimming. However gunzip command is not working on paired files. Any suggestions? this is the error output gzip: file.fastq.gz: unexpected end of file Thank you! Last edited by Kaskere; 09-01-2020 at 02:36 AM.

09-01-2020, 03:51 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Are you sure the files are gzipped (is spite of what the extension says)? What does Code: file one_file.fastq.gz say?

09-01-2020, 09:17 AM	#4
Biocomputronics Junior Member Location: USA Join Date: Sep 2017 Posts: 5	Try using "zcat" to see if it can display the file contents like: zcat file.fastq.gz If it displays the file contents, then redirect the output to a new file like: zcat file.fastq.gz > new_file.fastq

09-01-2020, 10:58 AM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	@kaskere: Were these files compressed using Windows zip program? You may need to use "-S .zip" option for gunzip.