Can't extract tar.gz

[f.pop]

Hi,

I was wondering if someone could help me. I am trying to extract a compressed file (.fq.tar.gz) and I constantly get the following message:

$ tar -xf ea179s_6_all.fq.tar.gz
../ea179s_6_all.fq: Path contains '..'
tar: Error exit delayed from previous errors.

Path looks like this:

/Users/Feri/Desktop/Klaus_Geider/Seq_raw/extr

therefore I don't get it why I get the: Path contains '..'

I already tried lots of combinations, like: tar xvf, tar -xvf, the -P option etc.

Thanx in advance,

[scd]

Not sure if you tried this yet, but when untarring a gzipped file you'll need the 'z' option.
E.g. tar -xzf ea179s_6_all.fq.tar.gz

[GenoMax]

Hi,

I was wondering if someone could help me. I am trying to extract a compressed file (.fq.tar.gz) and I constantly get the following message:

$ tar -xf ea179s_6_all.fq.tar.gz
../ea179s_6_all.fq: Path contains '..'
tar: Error exit delayed from previous errors.

Path looks like this:

/Users/Feri/Desktop/Klaus_Geider/Seq_raw/extr

therefore I don't get it why I get the: Path contains '..'

I already tried lots of combinations, like: tar xvf, tar -xvf, the -P option etc.

Thanx in advance,

You can also "gunzip" the file first and then untar it later.

[ffinkernagel]

I suspect that for some reason '../ea17'... is the file name stored in your tar archive.
What does tar -tfz ea179... output?

anyhow, it's a good idea to gunzip (or gzip -d) the file first to seperate whether the problem is the tar, or gzip, as these formats are basically nested.

[f.pop]

Not sure if you tried this yet, but when untarring a gzipped file you'll need the 'z' option.
E.g. tar -xzf ea179s_6_all.fq.tar.gz

I've tried it following your recommendation, but it didn't work...thx anyway

[f.pop]

I suspect that for some reason '../ea17'... is the file name stored in your tar archive.
What does tar -tfz ea179... output?

anyhow, it's a good idea to gunzip (or gzip -d) the file first to seperate whether the problem is the tar, or gzip, as these formats are basically nested.

The tar file contains 36bp reads (fastq) of a bacterial genome.
$ tar -tfz ea179s_6_all.fq.tar.gz gives me this (and tha path to the file is correct):
tar: Error opening archive: Failed to open 'z': No such file or directory

Gunzip worked fine, so we know that the gzip part is OK, but then again when I tried to untar the now already decompressed archive nothing happens. The system just hangs. I've tried :
$ tar -xf ea179s_6_all.fq.tar
or
$ tar -xvf ea179s_6_all.fq.tar
or
$ tar -cf ea179s_6_all.fq.tar

but nothing helped. Can it be that the file name stored in the archive is different from the one that I see now as ea179s_6_all.fq.tar? Since I got the files from a collaborator and maybe he uses Linux (I don't know), can it be that there are incompatibilities between my Mac system and his?

[GenoMax]

The tar file contains 36bp reads (fastq) of a bacterial genome.
$ tar -tfz ea179s_6_all.fq.tar.gz gives me this (and tha path to the file is correct):
tar: Error opening archive: Failed to open 'z': No such file or directory

Gunzip worked fine, so we know that the gzip part is OK, but then again when I tried to untar the now already decompressed archive nothing happens. The system just hangs. I've tried :
$ tar -xf ea179s_6_all.fq.tar
or
$ tar -xvf ea179s_6_all.fq.tar
or
$ tar -cf ea179s_6_all.fq.tar

but nothing helped. Can it be that the file name stored in the archive is different from the one that I see now as ea179s_6_all.fq.tar? Since I got the files from a collaborator and maybe he uses Linux (I don't know), can it be that there are incompatibilities between my Mac system and his?

f.pop,

I know this going to sound crazy but can you check with your collaborator if they made the tar files on a windows machine (64-bit)? I remember having trouble with tar files that were made on a windows machine before.

If you have access to a 64-bit windows machine you could try using a program like "7-zip" to see if you can untar the file there.

[f.pop]

f.pop,

I know this going to sound crazy but can you check with your collaborator if they made the tar files on a windows machine (64-bit)? I remember having trouble with tar files that were made on a windows machine before.

If you have access to a 64-bit windows machine you could try using a program like "7-zip" to see if you can untar the file there.

Thanx for the ideea, I'll try it. This could be the only explanation that's left.

[gringer]

$ tar -tfz ea179s_6_all.fq.tar.gz gives me this (and tha path to the file is correct):
tar: Error opening archive: Failed to open 'z': No such file or directory

This is because the ordering of the options are not what tar expects. the 'f' option must always be followed by a file name, so a better ordering would be this:

tar -tzf ea179s_6_all.fq.tar.gz

That will give you a listing of all the files in your archive. I suspect that the issue is that the files in the archive start with '/' (i.e. absolute location), and the usual process is to use relative locations when compressing / extracting (although looking at the help for the '-P' options in the tar man page, the default is to strip the leading '/'). If you want to explicitly strip the first specified directory (which may be '..'), then you can use the '--strip-components' option:

tar --strip-components=1 -xzf ea179s_6_all.fq.tar.gz

Note that since about 5 years ago (possibly longer), GNU tar is able to automatically determine whether the file was a gzipped or bzipped archive, so the z/b options aren't actually necessary on most Linux systems.