Hi everyone
I am trying to run Breseq but I keep getting the error shown in the image, no matter what type of data I use ( raw reads, trimmed, assemblies)
What could be the reason?
Thank you for any kind of help
Hi @davide_bersanetti
Click at Error icon, the one looking like ladybird beetle. Do you see the error message? If yes, is it useful?
Click at Info ( i ) icon. In the middle window scroll down and examine the standard output and standard error log files. Do you see any useful info (usually, at the end of log files)?
Try the tool with any suitable (tutorial) data. I don’t see any breseq tutorial at GTN, but data for Prokka can be used. Find Prokka in the took menu, and scroll down to Help section at the bottom of job setup page. You’ll see links to Prokka tutorials at GTN. You also can try Prokka on your data.
If all above does not help, maybe share the history, so people can check what is going on. History sharing: click at History options (three horizontal bars icon) at the top right corner of the history panel > Share or Publish > Make history accessible (in the middle window) > Copy the URL and paste it into reply.
Kind regards,
Igor
Good morning Igor,
Thank you for your prompt response.
In the Info part this is what I can see as a standard out put is: Backtrace with 11 stack frames. That is the only infomation
I also checked the beetle icon and this is what I can see, but what could it mean? I can see clearly my sequences on benchling/snapgene
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Seq id does not contain any valid alphanumeric characters.
FILE: libbreseq/reference_sequence.h LINE: 1192
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Picture of the dataset error report:
I will try to run through prokka my sequences ( I will have to do it anyhow) and try it again. But this breseq analysis is quite important so I will share the history URL.
https://usegalaxy.eu/u/db9638/h/wgs-first-batch
The Breseq runs that failed are visible in the deleted archive ( in the bin), but still visible.
If you could provide some assistance or insight, I would be extremely grateful.
admin reformatted
Hi Davide,
Thank you for the shared history.
Check breseq description in the Help section, at the bottom of the job setup page. The first sentence is:
breseq (pronounced: \brēz-ˈsēk\ or breeze-seq) is a computational pipeline for the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent, etc.).
You used assembly contigs as short reads. I suspect the tool cannot handle it.
Use data suitable for the tool.
You can unshare the history by switching Make history accessible to No.
Kind regards,
Igor
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