fastq.gz Error: Not in gzip format

Question

[V]

Hello,

I'm trying to run Hisat2 on 2 fastq files which are currently fastq.gz as downloaded from the servers of the people that did the sequencing for us. When I try to run it though, even though my code specifies fastq.gz, I keep getting the error that the files are not gziped.

This is the code im using :

hisat2 -p 7 -x -known-splicesite-infile /usr/local/src/gtf.gtf mm10idx -1 WTCHG_284763_229_1.fastq.gz -2 WTCHG_284763_229_2.fastq.gz -S eg2.bam

Any ideas? thanks

[GenoMax]

What do you get with these two commands file WTCHG_284763_229_1.fastq.gz or zmore WTCHG_284763_229_1.fastq.gz (ctrl+c to return to system prompt)?

[V]

it outputs this

--More--

is that good or bad? :/

[GenoMax]

What do you get for file WTCHG_284763_229_1.fastq.gz?

Based on your answer below it looks like these are compressed files but they may have been corrupted when you downloaded them. Can you try redownloading them? Did you change the file name in any way during the download?

[V]

file outputs this:

X11 SNF font data, MSB first

I've downloaded the files using filezilla which is usually fine but I'll try re-downloading from the server.

[GenoMax]

That would the the thing to try. I would suggest downloading the file using sftp directly on the server and taking out filezilla (as long as your server has a direct internet link).

[V]

I've checked the md5sum of the files and they don't match so something is going wrong with the files while they're being downloaded. Tried sftp and filezilla and both have mismatches. Any suggestions for alternatives? :/ Usually I've been using cyberduck but it completely doesn't work lately.

[V]

Found a questionable solution to this online and tried it anyway and it worked.

Apparently my firewall must be doing something to the files. Switched the firewall off and then downloaded the files and everything is ok! md5sums etc

[GenoMax]

Firewall on Win 10 or virtual box? It is interesting that the file contents are mangled by the firewall rather than just preventing you from connecting/downloading.

[V]

Firewall on both, downloaded via ubuntu - mangled, downloaded via windows 10 - mangled again. But after switching the firewall off and downloading via filezilla (in windows) everything worked fine.

Hisat2 is working fine on them aswell so no idea why the firewall being up would do that to the files. First time its happened because I've been using this machine/OS for over a year. Maybe it was something they changed in the recent update to windows10...

Answer 1

[Chris Miller]

Well, start by making sure that they're gzipped files and not just errantly named:

$ file tmp.gz
tmp.gz: gzip compressed data,was "tmp", from Unix, last modified: Tue Dec 13 13:12:02 2016, max compression

Also try opening it without unzipping

less file.gz

If the output comes back as non-gibberish, then you've got a standard text file that isn't actually gzipped. Remove the extension and gzip it yourself.

[V]

Couldn't get the first bit you wrote to work for some reason.

Opened it using your second command and it all came back gibberish.

[Chris Miller]

What OS are you using?

[V]

Windows 10 but running Ubuntu via virutalbox. All of the above are happening in ubuntu.

[Chris Miller]

"file" should be a valid command on just about any *nix system. Did it output an error or what?

[John]

Did you type "$" when you ran the first command?