Question: fastq.gz Error: Not in gzip format
0
gravatar for V
7 months ago by
V50
UK/London
V50 wrote:

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

hisat2 rnaseq • 532 views
ADD COMMENTlink modified 7 months ago by Chris Miller18k • written 7 months ago by V50

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)?

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax30k

it outputs this

--More--

is that good or bad? :/

ADD REPLYlink written 7 months ago by V50

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?

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax30k

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.

ADD REPLYlink written 7 months ago by V50

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).

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax30k

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.

ADD REPLYlink written 7 months ago by V50

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

ADD REPLYlink written 7 months ago by V50

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.

ADD REPLYlink written 7 months ago by genomax30k

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...

ADD REPLYlink written 7 months ago by V50
1
gravatar for Chris Miller
7 months ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

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.

ADD COMMENTlink written 7 months ago by Chris Miller18k

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.

ADD REPLYlink written 7 months ago by V50

What OS are you using?

ADD REPLYlink written 7 months ago by Chris Miller18k

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

ADD REPLYlink written 7 months ago by V50

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

ADD REPLYlink written 7 months ago by Chris Miller18k

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

ADD REPLYlink written 7 months ago by John11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 465 users visited in the last hour