There is a problem with computematrix (and maybe also other tools) when you choose a bedgraph file as an input. Galaxy will let you choose a “bedgraph (as bigwig)” file as an input but will then fail to run and will tell you that your input dataset is in an error state. At first I thought that somet…

Hi @TTP I see both tools at UseGalaxy.org today: One with the option for trimming overhanging coordinates (the version that is best to use after MACS2) → https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ucsc_wigtobigwig/ucsc_wigtobigwig/447+galaxy0 And one with the direct conve…

Hi @TTP This is interesting behavior. Is it still reproducible? I wondering if the converter tool is missing or has some new bug! If you want to isolate and share back an example history with the problem, we can confirm and reach out to the administrators to get it fixed. As an aside, I’ve seen s…

Yes, other people I know have had a similar problem. I just ran another job to illustrate this: [ Galaxy usegalaxy.org [favicon.ico] ]( https://usegalaxy.org/u/tpaull/h/hb155-to-hb174 ) The other problem that is visible in this history is that I am getting a lot of “used more memory than it was …

[image] TTP: https://usegalaxy.org/u/tpaull/h/hb155-to-hb174 Thanks, I’m reviewing. [image] TTP: getting a lot of “used more memory than it was allocated” errors these days Odd … this should be happening less frequently given recent boosts in resources. I see an example in your histor…

OK, this is what is going on: The version of the converter available from the tool panel includes an option to trim “overhanging coordinates”, instead of failing. It is toggled on by default. The version of the converter available from the “auto-convert” between the datatypes does not include a tr…

Thanks for this response. I am now always converting from the MACS2 output bedgraph to bigwig format directly using Wig/Bedgraph to bigwig, but today somehow the tool seems to have disappeared. There is a tool called “Convert Bedgraph to bigwig” but this is giving an error with my input files. Could…

Hi @TTP First, if you are working at UseGalaxy.org , please try a rerun now. The server was undergoing updates earlier and a few jobs randomly failed. Would you please clarify the following, then we can follow up about what might be going on? Tools shouldn’t be lost of course! The server URL wher…

Thanks. I am using usegalaxy.org and saw problems earlier but more recently it seems to be working fine apart from this problem. Previous tool was Wig/BedGraph-to-bigWig converter. Where did this go? tool that is failing is Convert Bedgraph to Bigwig. There were other errors earlier today, but th…

Hi @TTP Ok, I have more details. We have reorganized some of these functions to make the usage clearer As part of that, the tool you were using was hidden from the tool panel (on purpose) But since that results in a loss of functionality (overhang coordinate clip), we are installing it fully agai…

I have checked a few times but this tool is still not findable through its previous name; is it there under another name? Previously called Wig/BedGraph-to-bigWig converter Thanks

Hi @TTP This version of the tool should work. Be sure to assign a database to your datasets, and to use the advanced options to clip the overhang sequence. wigtobigwig bedGraph or Wig to bigWig converter link to tool

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tools that require bigwig input cannot use bedgraph (as bigwig) file

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