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}

0

I used zcat and gzip to merge and zip the files using:

zcat file1.fastq.gz file2.fastq.gz | gzip -c > file1.fastq.gz

Now, I have 0 bytes file1.fastq.gz

Please advise?

linux

share|improve this question

edited 18 hours ago

Attie

13.3k43649

asked 18 hours ago

raman sethiraman sethi

11

New contributor

raman sethi is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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add a comment | 

0

I used zcat and gzip to merge and zip the files using:

zcat file1.fastq.gz file2.fastq.gz | gzip -c > file1.fastq.gz

Now, I have 0 bytes file1.fastq.gz

Please advise?

linux

share|improve this question

edited 18 hours ago

Attie

13.3k43649

asked 18 hours ago

raman sethiraman sethi

11

New contributor

raman sethi is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

add a comment | 

I used zcat and gzip to merge and zip the files using:

zcat file1.fastq.gz file2.fastq.gz | gzip -c > file1.fastq.gz

Now, I have 0 bytes file1.fastq.gz

Please advise?

linux

share|improve this question

edited 18 hours ago

Attie

13.3k43649

asked 18 hours ago

raman sethiraman sethi

11

New contributor

raman sethi is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

zcat file1.fastq.gz file2.fastq.gz | gzip -c > file1.fastq.gz

share|improve this question

edited 18 hours ago

Attie

13.3k43649

asked 18 hours ago

raman sethiraman sethi

11

New contributor

raman sethi is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

edited 18 hours ago

Attie

13.3k43649

asked 18 hours ago

raman sethiraman sethi

11

New contributor

raman sethi is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

edited 18 hours ago

Attie

13.3k43649

edited 18 hours ago

Attie

13.3k43649

asked 18 hours ago

raman sethiraman sethi

11

New contributor

raman sethi is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

asked 18 hours ago

raman sethiraman sethi

11

1 Answer
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0

When you use the > redirection, the shell will open the named file (file1.fastq.gz) for writing and truncate it to zero length. (documentation)

Next, zcat will run, with file1.fastq.gz and file2.fastq.gz as input files .

At this point, zcat throws an error, because the input file (file1.fastq.gz) has no content - not even the GZip header - and the pipeline falls apart.

You may find that file1.fastq.gz is actually a few bytes in size (not zero), and this will be caused by gzip compressing and writing its null input.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file1.gz



gzip: file1.gz: unexpected end of file

$ stat -c '%s bytes' file1.gz

20 bytes

It's worth looking out for error messages like this.

---

There are a couple of viable solutions, but they depend on the size of your data.

In all situations, without some clever tricks, you will need to have enough space to store both the original and the new output file on disk at once.

Write to Another File

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file_all.gz

$ gzip -d < file_all.gz

foo

bar

Use sponge

If the data isn't too large, then the sponge utility will handle this situation for you. All data read from stdin is "soaked up" before any data is written to the output file.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c | sponge file1.gz

$ gzip -d < file1.gz

foo

bar

share|improve this answer

answered 17 hours ago

AttieAttie

13.3k43649

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you for your answer. You are right, it is not empty. I tried these commands but it didn't work
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is it possible to recover the old file? Thanks
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  The file 1 is 20 bytes while file 2 is 2.3GB, the file 1 was earlier 2.3 GB, i want to get both file 1 and file 2 as 2.3 GB
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  "Is it possible to recover the old file?" probably not... can you get / create it again?
  
  – Attie
  16 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  "is it possible to recover the old file?" superuser.com/questions/1124811/… superuser.com/questions/241817/…
  
  – ssice
  14 hours ago
  

  
  
  
  

add a comment | 

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0

When you use the > redirection, the shell will open the named file (file1.fastq.gz) for writing and truncate it to zero length. (documentation)

Next, zcat will run, with file1.fastq.gz and file2.fastq.gz as input files .

At this point, zcat throws an error, because the input file (file1.fastq.gz) has no content - not even the GZip header - and the pipeline falls apart.

You may find that file1.fastq.gz is actually a few bytes in size (not zero), and this will be caused by gzip compressing and writing its null input.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file1.gz



gzip: file1.gz: unexpected end of file

$ stat -c '%s bytes' file1.gz

20 bytes

It's worth looking out for error messages like this.

---

There are a couple of viable solutions, but they depend on the size of your data.

In all situations, without some clever tricks, you will need to have enough space to store both the original and the new output file on disk at once.

Write to Another File

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file_all.gz

$ gzip -d < file_all.gz

foo

bar

Use sponge

If the data isn't too large, then the sponge utility will handle this situation for you. All data read from stdin is "soaked up" before any data is written to the output file.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c | sponge file1.gz

$ gzip -d < file1.gz

foo

bar

share|improve this answer

answered 17 hours ago

AttieAttie

13.3k43649

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you for your answer. You are right, it is not empty. I tried these commands but it didn't work
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is it possible to recover the old file? Thanks
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  The file 1 is 20 bytes while file 2 is 2.3GB, the file 1 was earlier 2.3 GB, i want to get both file 1 and file 2 as 2.3 GB
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  "Is it possible to recover the old file?" probably not... can you get / create it again?
  
  – Attie
  16 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  "is it possible to recover the old file?" superuser.com/questions/1124811/… superuser.com/questions/241817/…
  
  – ssice
  14 hours ago
  

  
  
  
  

add a comment | 

0

When you use the > redirection, the shell will open the named file (file1.fastq.gz) for writing and truncate it to zero length. (documentation)

Next, zcat will run, with file1.fastq.gz and file2.fastq.gz as input files .

At this point, zcat throws an error, because the input file (file1.fastq.gz) has no content - not even the GZip header - and the pipeline falls apart.

You may find that file1.fastq.gz is actually a few bytes in size (not zero), and this will be caused by gzip compressing and writing its null input.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file1.gz



gzip: file1.gz: unexpected end of file

$ stat -c '%s bytes' file1.gz

20 bytes

It's worth looking out for error messages like this.

---

There are a couple of viable solutions, but they depend on the size of your data.

In all situations, without some clever tricks, you will need to have enough space to store both the original and the new output file on disk at once.

Write to Another File

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file_all.gz

$ gzip -d < file_all.gz

foo

bar

Use sponge

If the data isn't too large, then the sponge utility will handle this situation for you. All data read from stdin is "soaked up" before any data is written to the output file.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c | sponge file1.gz

$ gzip -d < file1.gz

foo

bar

share|improve this answer

answered 17 hours ago

AttieAttie

13.3k43649

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you for your answer. You are right, it is not empty. I tried these commands but it didn't work
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is it possible to recover the old file? Thanks
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  The file 1 is 20 bytes while file 2 is 2.3GB, the file 1 was earlier 2.3 GB, i want to get both file 1 and file 2 as 2.3 GB
  
  – raman sethi
  17 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  "Is it possible to recover the old file?" probably not... can you get / create it again?
  
  – Attie
  16 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  "is it possible to recover the old file?" superuser.com/questions/1124811/… superuser.com/questions/241817/…
  
  – ssice
  14 hours ago
  

  
  
  
  

add a comment | 

When you use the > redirection, the shell will open the named file (file1.fastq.gz) for writing and truncate it to zero length. (documentation)

Next, zcat will run, with file1.fastq.gz and file2.fastq.gz as input files .

At this point, zcat throws an error, because the input file (file1.fastq.gz) has no content - not even the GZip header - and the pipeline falls apart.

You may find that file1.fastq.gz is actually a few bytes in size (not zero), and this will be caused by gzip compressing and writing its null input.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file1.gz



gzip: file1.gz: unexpected end of file

$ stat -c '%s bytes' file1.gz

20 bytes

It's worth looking out for error messages like this.

---

There are a couple of viable solutions, but they depend on the size of your data.

In all situations, without some clever tricks, you will need to have enough space to store both the original and the new output file on disk at once.

Write to Another File

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file_all.gz

$ gzip -d < file_all.gz

foo

bar

Use sponge

If the data isn't too large, then the sponge utility will handle this situation for you. All data read from stdin is "soaked up" before any data is written to the output file.

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c | sponge file1.gz

$ gzip -d < file1.gz

foo

bar

share|improve this answer

answered 17 hours ago

AttieAttie

13.3k43649

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file1.gz



gzip: file1.gz: unexpected end of file

$ stat -c '%s bytes' file1.gz

20 bytes

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c > file_all.gz

$ gzip -d < file_all.gz

foo

bar

$ echo "foo" | gzip > file1.gz

$ echo "bar" | gzip > file2.gz

$ zcat file1.gz file2.gz | gzip -c | sponge file1.gz

$ gzip -d < file1.gz

foo

bar

share|improve this answer

answered 17 hours ago

AttieAttie

13.3k43649

answered 17 hours ago

AttieAttie

13.3k43649

answered 17 hours ago

AttieAttie

13.3k43649