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thanks Björn
Hope you are doing fine! Long time ... :)
I have a collection of many samples that I ran fastp on (on .eu) - some jobs failed with the cryptic error message "Unable to finish job" and nothing in stderr. What is the easiest way to select all the failed datasets and re-run them to see if they succeed a second time?
There is an API to restart all failed jobs in a history and it's in bioblend
If that does not work you need to reload all failed jobs and click rerun inplace
I'm trying to help out a colleague who is doing Galaxy 101 but one of their jobs failed with the message "Unable to finish job". This is history ID 0876ff39fabc4ccd - is there something wrong with the server?
I just tried re-running the job and got a new error - "cat: write error: Broken pipe" - this is an error reported in the stderr (whereas the previous one had empty stderr) but again it looks strange to me
I am trying to move a history from usegalaxy.eu to usegalaxy.org. I exported on .eu and have a link, but when I try and use that to import to .org I get a 403: Forbidden error. is there some setting I am meant to change to make the exported link accessible?
ok, looks like this was two different errors, with one masking the other.
the original error was "Unable to finish job" - then when that went away the "cat: write error: Broken pipe" showed up. The second error is happening with version 1.0.1 of the "Show beginning1" tool but "text_processing/tp_head_tool" version 1.1.0 - the tool that should be used for the Galaxy 101 tutorial - works
both tools are, however, called "Select first lines from a dataset".
That rings a bell
I will look at it
bgruening the earlier "Unable to finish job" error though - do you think that was the tool or the server? I've been getting them sporadically with a bunch of different tools.
But when I was trying to look at them in deep I could not see anything failing anymore
and do you have a solution to my problem exporting from .eu to .org? seems the .org server is not allowed to download my .eu-generated history archive link.
sorry lots of questions from me today
Is it public?
No I don't know.
I can only download from the link when logged into the Galax server. I made the link by choosing the "Export history archive" and "to a link" options. So I can download this archive to my local PC and re-upload - it is large though so this is not practical. I am using the procedure documented here: https://training.galaxyproject.org/training-material/faqs/galaxy/histories_transfer_entire_histories_from_one_galaxy_server_to_another.html
perhaps this is not a .eu specific issue though. let me test this with another set of servers
verified that this fails for other combinations of servers (SANBI Galaxy -> .org for example)
Can you download the link from a different computer or when you are logged out?
I get the error ""History is not accessible by user" - so I dont think this link-based export / import works.
I suspect this link should be public but it's not
bug report where? on Galaxy issues? because this does not seem to be .eu specific
This sounds pretty familiar to me; I thought we had automatically made these accessible. +1 to making an issue and we can make sure it gets looked at.
The error message looks like a) wrong or unexpected inputs, b) no search results and a later step fails because there are no results to process
@ZhouHY-77: thanks for the report. It really looks like that the BLAST step in the Staramr tool is not yielding any result. The tool should yield a better error, but thtat is nothing we can fix.