Error During Data Upload Of Fastq.Gz

Question: Error During Data Upload Of Fastq.Gz

6.8 years ago by

hi, Maybe anybody can give me a hint for the following problem... When I try to upload a fastq.gz file into galxy using url function the input os canceled with the following exception: An error occurred running this job: The uploaded file contains inappropriate HTML content I don't know where to start to have a look at. The upload of all other fastq.gz files from the same run works smooth. best stefan PS. Yes I know, the problem is really unspecific, sorry for that...

• 1.3k views

ADD COMMENT • link •

modified 6.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.8 years ago by Stefan Kroeger • 30

6.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Stefan, Are you still having this problem? One thought is that this file is some sort of README file in with the other data files from you source. Another is that the data is an annotation file, not a sequence file, with one or more columns of data in HTML format. Some things to check: - have you opened/uncompressed the file locally to see if it contains any HTML? - are you able to download, uncompress, and then load the file uncompressed or does that also give errors? Using "upload from the desktop" or "FTP"? Please let us know if you are still having problems and what happens when you try these tests. We would be very interested in correcting any problems with valid files being rejected for some odd reason, so please include the URL to the problem file in your reply. Thank you! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 6.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, yes I still have the problem, but to ensure it's not a file error I will check the original data from the lab. if the problem is still present I will come back to you. it's a complete lane so really hard to check by eye ;-) do you know any kind of "command line fasta validation tool"? tried both, no changes. Thanks & best regards Stefan

ADD REPLY • link written 6.8 years ago by Stefan Kroeger • 30

Hi Stefan, Could you upload it to the FTP site and then send us the filename, without attempting to import it using the "Upload File" tool in the web interface? I'll grab a copy and take a look at it. --nate

ADD REPLY • link written 6.8 years ago by Nate Coraor ♦ 3.2k

2012/1/30 Nate Coraor <nate@bx.psu.edu> unfortunately not, I'm not allowed to. but thanks for your help. best Stefan

ADD REPLY • link written 6.8 years ago by Stefan Kroeger • 30

Is this in a local instance, then? You'll have to take a look at tools/data_source/upload.py and have a look at the html checks to see where and why it's failing. Have you checked the first and last lines of the file? That's occasionally the problem. --nate

ADD REPLY • link written 6.8 years ago by Nate Coraor ♦ 3.2k

Similar posts • Search »