# QUAST ERROR. Can someone offer guidence? **URL:** \ **Category:** usegalaxy.org support\ **Tags:** troubleshooting, genome-annotation\ **Created:** [March 15, 2025, 9:24pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013 "2025-03-15T21:24:54Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 15, 2025, 9:24pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/1 "2025-03-15T21:24:54Z")
Hi everyone. I am running QUAST on metagenome assemblies from MEGAHIT, and my job keeps failing with the following error: Fatal error: Exit code 1 ()! I have set it up like this: Input: “Assembly on Collection” from MEGAHIT Type of assembly: Metagenome Reference Genome\*\*:\*\* SILVA database Minimum contig length = 500 bp Max reference genomes = 50 Assembly Mode: Co-assembly (1 contig file for several samples) Reads: “Illumina paired-end reads in paired collection” FASTQ/FASTA Input: "seqtk\_sample on collection " Type of Assembly: Metagenome Reference Genome: SILVA database Max Reference Genomes: 50 Alignment Identity Threshold: 90% Min Contig Length: 500 bp Are assemblies scaffolds rather than contigs: No Is genome large: No I do not know what the issue is. Can someone advise? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2025, 6:06pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/2 "2025-03-17T18:06:28Z")
Hello @Martyn Thanks for sharing all of these details! 🙂 Check your job logs in the **Job Details** view ([using the i-info icon](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_icons.html)). Is the job failing for memory reasons? Like this topic below? > [@Resolving memory failures with SPAdes](https://help.galaxyproject.org/t/resolving-memory-failures-with-spades/13322/2): > > Error message > > > This job was terminated because it used more memory than it was allocated. > > If an assembly is running out of processing memory during execution, there are a few things you can do. > > **Use Case** > The current work is running out of [processing memory during job execution](https://training.galaxyproject.org/training-material/faqs/galaxy/troubleshooting_excess_memory.html). This is different from the [data storage available in your account](https://help.galaxyproject.org/docs?topic=13193). > > **What to try** > > - Run the [reads through quality control](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html) to improve the content the tool is attempting to assemble. > - Set more input parameters to improve how the tool is attempting to assemble. > - Reduce the number of reads submitted with a tool like **Sub-sample sequences**. Some protocols involve pre-clustering with other strategies, too. > - Try at a different public server. Each hosts distinct resources. * * * For your use case, since you are already filtering for the contig length with this Quast parameter setting: > [@Martyn](#): > > Minimum contig length = 500 bp You could try pre-filtering the lengths first to reduce the size of the input data, and maybe avoid this error? - Search the tool panel for: **Filter sequences by length** - You can run this on the entire collection. If some of the samples are now empty, you might need to then run **Filter empty datasets** before running Quast. If you want to share your history, we might be able to suggest more pre-steps or different Quast parameters to try. Thanks! Xref → [How to get faster help with your question](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469) ---
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 17, 2025, 8:19pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/3 "2025-03-17T20:19:57Z")
Hi JennaJ, thank you for helping me again. It says that it ran longer than the allowed run time so i am not sure it is a memory issue? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2025, 10:40pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/4 "2025-03-17T22:40:15Z")
Ok, thanks for clarifying @Martyn, the memory error was a guess since it is more common. If the error instead states the job is exceeding runtime resources, that is a bit different for the root cause, but still the same result with similar solutions. The EU server doesn’t apply walltime at all but they will eventually kill runaway jobs. Does this help? - [FAQ: Understanding walltime error messages](https://training.galaxyproject.org/training-material/faqs/galaxy/troubleshooting_walltime.html) - More variations are here (including the memory reason). → [Galaxy FAQs](https://training.galaxyproject.org/training-material/faqs/galaxy/#troubleshooting) ---
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 18, 2025, 11:21am UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/5 "2025-03-18T11:21:57Z")
Hi JennaJ, how do I do it on the EU server. Do i need to submit my Assembly with MEGAHIT on collection to the EU version or do i have to start it all over again? Best wishes ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 18, 2025, 6:49pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/6 "2025-03-18T18:49:02Z")
Hi @Martyn You do not need to start over! 🙂 Instead, you can copy the data you want to move over into a new smaller history on the “from” server, then move that history over to the “to” server. You can also move individual files if you ever need to. Help → [FAQ: Transfer entire histories from one Galaxy server to another](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_transfer_entire_histories_from_one_galaxy_server_to_another.html) ---
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 20, 2025, 3:04am UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/7 "2025-03-20T03:04:36Z")
Hi JennaJ, thank you for your help. i am having the same problems again with a fatal error eve on the EU server. Should i subsample the sequences? ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/36255018598b0de051b1696d471fa57b61171d90.png) ---
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 21, 2025, 11:35am UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/8 "2025-03-21T11:35:16Z")
Hi everyone, I have tried subsampling the data on the EU server and I am still getting the same error message. This is really frustrating as i have tried everything now. Is the issue QUAST itself? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 21, 2025, 8:43pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/9 "2025-03-21T20:43:30Z")
Hi @Martyn What happens if your run a tool like **Fasta Statistics** on the data? Can that tool understand the data in your collections or does it report a problem? If it runs, does anything else look unexpected in the summary? I am also curious about what happens if you try to run on just one genome file? You are welcome to share the EU history back. Please leave the subset and statistics job in there too please. Maybe we can help to recognize what the problem is. How to share is in the banner of this forum, also here → [How to get faster help with your question](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469) Thanks! 🙂 ---
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 23, 2025, 11:45pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/11 "2025-03-23T23:45:05Z")
Hi JennaJ , This link should work? > **[Galaxy](https://usegalaxy.eu/published/history?id=3483ed0aa2aa44a7)** > > Galaxy is a community-driven web-based analysis platform for life science research. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 24, 2025, 5:46pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/12 "2025-03-24T17:46:23Z")
Great, thanks for sharing the history @Martyn In the job logs (using the i-con), I see the root message. ```auto Text versions of reports and plots for each metric (for all references and assemblies) are saved to /data/jwd06/main/080/801/80801793/working/outputdir/summary/ Icarus (contig browser) is saved to /data/jwd06/main/080/801/80801793/working/outputdir/icarus.html Drawing interactive Krona plots... WARNING: Error occurred while build Krona charts, skipping... You can disable drawing Krona (and thus, this warning) with "--no-krona". Extended version of HTML-report (for all references and assemblies) is saved to /data/jwd06/main/080/801/80801793/working/outputdir/report.html ``` The tool is having trouble processing one of the output files, specifically the Krona plot. But it also states that the step was skipped. Confusing! I’m rerunning with that option not selected to see what happens. Maybe the other log files will be informative. This is the link to that history. We can follow up more once it is completed. (some reports are already produced) - [https://usegalaxy.eu/u/jenj/h/ghelp-15013-quast-copy-of-unnamed-history-https-help-galaxyproject-org-t-quast-error-can-someone-offer-guidence-15013-9](https://usegalaxy.eu/u/jenj/h/ghelp-15013-quast-copy-of-unnamed-history-https-help-galaxyproject-org-t-quast-error-can-someone-offer-guidence-15013-9) ---
**Author:** ![Martyn](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Post date:** [March 25, 2025, 9:49pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/13 "2025-03-25T21:49:17Z")
Hi JennaJ, thank you very much. it looks like it had worked here in your link? Did you do anything different to me? Best wishes ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 31, 2025, 6:55pm UTC](https://help.galaxyproject.org/t/quast-error-can-someone-offer-guidence/15013/14 "2025-03-31T18:55:33Z")
Hi @Martyn I set different output parameters. You can review what I did versus what you did by comparing the job details pages from the different runs (these summarize the parameters used each time). From that result (HTML report), the underlying problem seems to be that the assembly for some accessions didn’t work very well, resulting in too many contigs for the Krona chart tool to handle. You could leave those out and try running this with just the successful assemblies?