Error during data upload of fastq.gz
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...
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 On 1/26/12 5:55 AM, Stefan Kroeger wrote:
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... ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Jen, On 30.01.2012 16:12, Jennifer Jackson wrote:
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.
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.
Some things to check: - have you opened/uncompressed the file locally to see if it contains any HTML?
it's a complete lane so really hard to check by eye ;-) do you know any kind of "command line fasta validation tool"?
- 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"?
tried both, no changes. Thanks & best regards Stefan
[...]
On 1/26/12 5:55 AM, Stefan Kroeger wrote:
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... ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Jan 30, 2012, at 11:37 AM, Stefan Kroeger wrote:
Hi Jen,
On 30.01.2012 16:12, Jennifer Jackson wrote:
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.
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.
Some things to check: - have you opened/uncompressed the file locally to see if it contains any HTML?
it's a complete lane so really hard to check by eye ;-) do you know any kind of "command line fasta validation tool"?
- 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"?
tried both, no changes.
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
Thanks & best regards Stefan
[...]
On 1/26/12 5:55 AM, Stefan Kroeger wrote:
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... ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
2012/1/30 Nate Coraor <nate@bx.psu.edu>
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.
unfortunately not, I'm not allowed to. but thanks for your help. best Stefan
On Jan 31, 2012, at 3:46 AM, Stefan Kroeger wrote:
2012/1/30 Nate Coraor <nate@bx.psu.edu> 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.
unfortunately not, I'm not allowed to. but thanks for your help.
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
best Stefan ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Jennifer Jackson -
Nate Coraor -
Stefan Kroeger