Question: fastq.gz files receiving error (Problem decompressing)
0
gravatar for simranmaggo
2.5 years ago by
New Zealand
simranmaggo0 wrote:

I uploaded 8 fastq.gz files. Two decompressed fine upon upload the remaining six say:

Problem decompressing gzipped data

Can someone please advise on how to fix this? Decompressing of the files works fine on my computer.

Thanks.

software error fastq.gz • 829 views
ADD COMMENTlink modified 2.4 years ago • written 2.5 years ago by simranmaggo0

For Galaxy to be able to decompress each archive needs to consist of exactly one file. Is that true for your archives?

ADD REPLYlink written 2.4 years ago by Martin Čech ♦♦ 4.3k

Yes there is only one file, I have checked by locally decompressing the file. I think there seems to be some issue while uploading, I have tried a few times with some other files and it works after a few goes. Suspecting perhaps the files are getting corrupted during upload.

ADD REPLYlink written 2.4 years ago by simranmaggo0

How large are the files that give you problems?

ADD REPLYlink written 2.4 years ago by Martin Čech ♦♦ 4.3k

1.7 GB

I have contacted the company who did the exomes for us to check the file. I have managed to upload the rest to galaxy successfully, one file keeps giving an error (as described in my original post).

ADD REPLYlink written 2.4 years ago by simranmaggo0

Did you try uploading them through the FTP or just through the browser?

ADD REPLYlink written 2.4 years ago by Martin Čech ♦♦ 4.3k

I have tried both FTP and direct file uploading.

As I mentioned above I have a sneaky feeling perhaps there is something wrong with the compression of the file, and have contacted the company who did the exomes to double check.

Thanks,

ADD REPLYlink written 2.4 years ago by simranmaggo0

The issue is now resolved. I was forwarded a new .gz file which I uploaded and it seemed to work fine.

Thank you.

ADD REPLYlink written 2.4 years ago by simranmaggo0
0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Suspected data corruption upstream of Galaxy. See comments.

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson23k
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 16.09
Traffic: 102 users visited in the last hour