# \#exceeds-memory-error **URL:** https://help.galaxyproject.org/tag/exceeds-memory-error/385.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Requested memory issues](https://help.galaxyproject.org/t/requested-memory-issues/18430)
**Author:** [@bsegers](https://help.galaxyproject.org/u/bsegers)\ **Replies:** 1\ **Last updated:** [September 30, 2026, 4:30pm UTC](https://help.galaxyproject.org/t/requested-memory-issues/18430 "2026-09-30T16:30:05Z")
It’s been three weeks now that I haven’t been able to get any results using the GetOrganelle tool : Get organelle from reads (version 1.7.7.1+galaxy0). I keep getting the same error message about the requested memory. "… --- ## [Lotus2 failing because it 'used more memory than it was allocated' but 90% of storage space is free](https://help.galaxyproject.org/t/lotus2-failing-because-it-used-more-memory-than-it-was-allocated-but-90-of-storage-space-is-free/18144)
**Author:** [@raphbow](https://help.galaxyproject.org/u/raphbow)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 2:42am UTC](https://help.galaxyproject.org/t/lotus2-failing-because-it-used-more-memory-than-it-was-allocated-but-90-of-storage-space-is-free/18144 "2026-07-06T02:42:13Z")
Hi there, I am running the Lotus2 tool with multiple fastq files. When I include the whole dataset (27 fastq files) the job fails with the error message, ‘This job was terminated because it used more memory than it wa… --- ## [\[samtools fixmate\] memory allocation error](https://help.galaxyproject.org/t/samtools-fixmate-memory-allocation-error/17656)
**Author:** [@angelo\_chan](https://help.galaxyproject.org/u/angelo_chan)\ **Replies:** 5\ **Last updated:** [April 27, 2026, 11:14pm UTC](https://help.galaxyproject.org/t/samtools-fixmate-memory-allocation-error/17656 "2026-04-27T23:14:21Z")
The Problem When I get to the \[samtools fixmate\] step of my workflow, I always get a samtools sort: couldn’t allocate memory for bam\_me … error. My Amateur Troubleshooting Attempts Disclaimer: I am not an expert at de… --- ## [This job was terminated because it used more memory than it was allocated. How to troubleshoot!](https://help.galaxyproject.org/t/this-job-was-terminated-because-it-used-more-memory-than-it-was-allocated-how-to-troubleshoot/17465)
**Author:** [@courageibo11](https://help.galaxyproject.org/u/courageibo11)\ **Replies:** 1\ **Last updated:** [February 17, 2026, 10:02pm UTC](https://help.galaxyproject.org/t/this-job-was-terminated-because-it-used-more-memory-than-it-was-allocated-how-to-troubleshoot/17465 "2026-02-17T22:02:34Z")
Message - his job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help. What can I do --- ## [Job still running for more than 15 hours](https://help.galaxyproject.org/t/job-still-running-for-more-than-15-hours/17405)
**Author:** [@Monish\_V](https://help.galaxyproject.org/u/Monish_V)\ **Replies:** 9\ **Last updated:** [February 11, 2026, 8:32pm UTC](https://help.galaxyproject.org/t/job-still-running-for-more-than-15-hours/17405 "2026-02-11T20:32:31Z")
I’ve been running HISAT on the given below job API ID Kindly provide support | 11ac94870d0bb33a951ae66565734a8e --- ## [Job running for more than an hour](https://help.galaxyproject.org/t/job-running-for-more-than-an-hour/17422)
**Author:** [@Adhiti\_R](https://help.galaxyproject.org/u/Adhiti_R)\ **Replies:** 1\ **Last updated:** [February 5, 2026, 6:33pm UTC](https://help.galaxyproject.org/t/job-running-for-more-than-an-hour/17422 "2026-02-05T18:33:47Z")
Any admins present kindly check and allocate more memory if possible | 11ac94870d0bb33a0c7895567614c98b --- ## [MultiQC issue creating flat plots](https://help.galaxyproject.org/t/multiqc-issue-creating-flat-plots/16528)
**Author:** [@grwtz](https://help.galaxyproject.org/u/grwtz)\ **Replies:** 3\ **Last updated:** [December 2, 2025, 3:33am UTC](https://help.galaxyproject.org/t/multiqc-issue-creating-flat-plots/16528 "2025-12-02T03:33:36Z")
Hi all, I was wondering if anyone has had issues using MultiQC– it works perfectly fine when I run it to create interactive plots but whenever I re-run to create flat plots, I get a disk quota exceeded error (even thoug… --- ## [Memory error with rnaSPAdes? Try QA/QC and Sub-sample sequences](https://help.galaxyproject.org/t/memory-error-with-rnaspades-try-qa-qc-and-sub-sample-sequences/16326)
**Author:** [@vishal\_jha](https://help.galaxyproject.org/u/vishal_jha)\ **Replies:** 1\ **Last updated:** [September 30, 2025, 5:52pm UTC](https://help.galaxyproject.org/t/memory-error-with-rnaspades-try-qa-qc-and-sub-sample-sequences/16326 "2025-09-30T17:52:15Z")
I am facing issue with rnaspades, it is not working for some of the data while format of all the data that I am using is corect --- ## [This job was terminated because itused more memory than it wasallocated](https://help.galaxyproject.org/t/this-job-was-terminated-because-itused-more-memory-than-it-wasallocated/15297)
**Author:** [@1263201095](https://help.galaxyproject.org/u/1263201095)\ **Replies:** 1\ **Last updated:** [April 25, 2025, 4:40pm UTC](https://help.galaxyproject.org/t/this-job-was-terminated-because-itused-more-memory-than-it-wasallocated/15297 "2025-04-25T16:40:12Z")
I used the tool ‘Scanpy FilterCells’, but the result showed that it exceeded memory. However, I believe the number of cells is not that large, as shown in the image below. How could this issue occur? Thank you! --- ## [SPADes and MEGAHIT memory issues](https://help.galaxyproject.org/t/spades-and-megahit-memory-issues/14947)
**Author:** [@Martyn](https://help.galaxyproject.org/u/Martyn)\ **Replies:** 1\ **Last updated:** [March 10, 2025, 4:48pm UTC](https://help.galaxyproject.org/t/spades-and-megahit-memory-issues/14947 "2025-03-10T16:48:51Z")
Hi, I am in the next step of my analysis and the jobs are just not completing for either of these. The error is an out of memory error. I have 5 samples. Does anyone know what to do about this? Best wishes --- ## [Resolving memory failures with SPAdes](https://help.galaxyproject.org/t/resolving-memory-failures-with-spades/13322)
**Author:** [@David\_Read](https://help.galaxyproject.org/u/David_Read)\ **Replies:** 1\ **Last updated:** [August 27, 2024, 5:30pm UTC](https://help.galaxyproject.org/t/resolving-memory-failures-with-spades/13322 "2024-08-27T17:30:29Z")
Hi everyone. What is the maximum number of paired-end reads that can be used as an input for a SPAdes assembly to avoid getting a “dataset too large” error? Thanks! --- ## [SPAdes error -- running out of memory/not enough memory allocated for job](https://help.galaxyproject.org/t/spades-error-running-out-of-memory-not-enough-memory-allocated-for-job/12654)
**Author:** [@Daniel\_Hogan](https://help.galaxyproject.org/u/Daniel_Hogan)\ **Replies:** 1\ **Last updated:** [June 6, 2024, 9:15pm UTC](https://help.galaxyproject.org/t/spades-error-running-out-of-memory-not-enough-memory-allocated-for-job/12654 "2024-06-06T21:15:06Z")
Hi, I am trying to run SPAdes for genome assembly but get error below which I think means it is running out of memory. Job Message 1: desc: Fatal error: Exit code 250 () error\_level: 3 exit\_code: 250 type: exit\_code … --- ## [Workflow troubleshooting post release 24.2](https://help.galaxyproject.org/t/workflow-troubleshooting-post-release-24-2/14730)
**Author:** [@mmb\_zorgregio](https://help.galaxyproject.org/u/mmb_zorgregio)\ **Replies:** 9\ **Last updated:** [February 25, 2025, 12:18am UTC](https://help.galaxyproject.org/t/workflow-troubleshooting-post-release-24-2/14730 "2025-02-25T00:18:50Z")
Hi, We are suddenly experiencing two errors in our workflow which used to work fine. We are getting the same error in fastP as well as Medaka on two different accounts. Is there an explanation for these errors? Both acc… --- ## [Proteogenomics fasta file generation w CustomProDB](https://help.galaxyproject.org/t/proteogenomics-fasta-file-generation-w-customprodb/14700)
**Author:** [@Odysseus\_1](https://help.galaxyproject.org/u/Odysseus_1)\ **Replies:** 2\ **Last updated:** [February 15, 2025, 2:00am UTC](https://help.galaxyproject.org/t/proteogenomics-fasta-file-generation-w-customprodb/14700 "2025-02-15T02:00:23Z")
Hi, I’m new to Galaxy and trying to create a FASTA file from transcriptomics data. However, I’m encountering an error when using CustomProDB: “This job has terminated because it used more memory than it was allocated. … --- ## [Minimap2 Memory Issue with hg38/T2T on Galaxy](https://help.galaxyproject.org/t/minimap2-memory-issue-with-hg38-t2t-on-galaxy/14739)
**Author:** [@jagoda\_33](https://help.galaxyproject.org/u/jagoda_33)\ **Replies:** 1\ **Last updated:** [February 14, 2025, 9:43pm UTC](https://help.galaxyproject.org/t/minimap2-memory-issue-with-hg38-t2t-on-galaxy/14739 "2025-02-14T21:43:42Z")
Hi everyone, I successfully ran Minimap2 on Galaxy using my viral reference genome and FASTQ.gz reads without any issues. However, when I try to run it with hg38 or T2T as the reference genome using the same FASTQ.gz in… --- ## [MarkDuplicates- inadequate memory](https://help.galaxyproject.org/t/markduplicates-inadequate-memory/14693)
**Author:** [@DHowell23](https://help.galaxyproject.org/u/DHowell23)\ **Replies:** 1\ **Last updated:** [February 10, 2025, 8:48pm UTC](https://help.galaxyproject.org/t/markduplicates-inadequate-memory/14693 "2025-02-10T20:48:38Z")
Hello, I am attempting to use markduplicates on my data aligned and sorted by Bowtie2. Everytime I attempt to run this tool, I receive the error detailed below. “The job terminated because it used more memory than alloc… --- ## [Troubleshooting Snippy memory allocation error](https://help.galaxyproject.org/t/troubleshooting-snippy-memory-allocation-error/14646)
**Author:** [@P.A.P\_KUMARA](https://help.galaxyproject.org/u/P.A.P_KUMARA)\ **Replies:** 1\ **Last updated:** [February 4, 2025, 9:11pm UTC](https://help.galaxyproject.org/t/troubleshooting-snippy-memory-allocation-error/14646 "2025-02-04T21:11:01Z")
I encountered an error while running Snippy with a GenBank reference and two raw reads. Any suggestions? what I should do …? Error is denote as “It used more memory than it was allocate” . (Galaxy.org) --- ## [Diffbind memory issues](https://help.galaxyproject.org/t/diffbind-memory-issues/14424)
**Author:** [@readlikeabook](https://help.galaxyproject.org/u/readlikeabook)\ **Replies:** 9\ **Last updated:** [January 15, 2025, 8:59pm UTC](https://help.galaxyproject.org/t/diffbind-memory-issues/14424 "2025-01-15T20:59:12Z")
Hi GalaxyHelp Group, I am trying to run a Diffbind analysis using previously-successful parameters and have submitted a series of “bug” reports over the last 4-5 days without a response-- figured it may be best to reach… --- ## [libjemalloc.so.2: cannot allocate memory in static TLS block Error on Galaxy Startup](https://help.galaxyproject.org/t/libjemalloc-so-2-cannot-allocate-memory-in-static-tls-block-error-on-galaxy-startup/13904)
**Author:** [@mochi7777](https://help.galaxyproject.org/u/mochi7777)\ **Replies:** 1\ **Last updated:** [November 13, 2024, 10:47pm UTC](https://help.galaxyproject.org/t/libjemalloc-so-2-cannot-allocate-memory-in-static-tls-block-error-on-galaxy-startup/13904 "2024-11-13T22:47:49Z")
When attempting to start Galaxy, the following error occurs: libjemalloc.so.2: cannot allocate memory in static TLS block This error leads to the failure of Galaxy’s job handler process and other components. This issue… --- ## [RNA STARSolo out of memory: where to adjust memory/node?](https://help.galaxyproject.org/t/rna-starsolo-out-of-memory-where-to-adjust-memory-node/13727)
**Author:** [@Stephanie\_Dv](https://help.galaxyproject.org/u/Stephanie_Dv)\ **Replies:** 3\ **Last updated:** [November 4, 2024, 7:01pm UTC](https://help.galaxyproject.org/t/rna-starsolo-out-of-memory-where-to-adjust-memory-node/13727 "2024-11-04T19:01:58Z")
Hi, I got this error. “This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help”. There does not seem to be anything wrong with the inp… --- ## [Trinity assembly failure](https://help.galaxyproject.org/t/trinity-assembly-failure/13693)
**Author:** [@David\_Morse](https://help.galaxyproject.org/u/David_Morse)\ **Replies:** 7\ **Last updated:** [October 29, 2024, 5:34pm UTC](https://help.galaxyproject.org/t/trinity-assembly-failure/13693 "2024-10-29T17:34:22Z")
Trying Trinity on paired end reads after Trim Galore does not work. I get an error, but am not sure how to solve the issue given the information it supplies. CernVM-FS: loading Fuse module… done CernVM-FS: mounted cvmf… --- ## [Targetfinder encountering error because it "uses more memory than allowed" (I don't think this is true); other strategies?](https://help.galaxyproject.org/t/targetfinder-encountering-error-because-it-uses-more-memory-than-allowed-i-dont-think-this-is-true-other-strategies/13479)
**Author:** [@tana](https://help.galaxyproject.org/u/tana)\ **Replies:** 1\ **Last updated:** [September 18, 2024, 4:19pm UTC](https://help.galaxyproject.org/t/targetfinder-encountering-error-because-it-uses-more-memory-than-allowed-i-dont-think-this-is-true-other-strategies/13479 "2024-09-18T16:19:06Z")
Hello! I am trying to map a small RNA database to a transcript in order to find sRNAs that may have originated from the transcript (identifying phasiRNAs). I am using 2.4GB total for both sets of data. I am trying to use… --- ## [Optimizing STAR Mapping for Large-Scale Genome Annotation: Managing Memory Overflows in RNA-Seq Workflows](https://help.galaxyproject.org/t/optimizing-star-mapping-for-large-scale-genome-annotation-managing-memory-overflows-in-rna-seq-workflows/13319)
**Author:** [@Naibin\_Duan](https://help.galaxyproject.org/u/Naibin_Duan)\ **Replies:** 6\ **Last updated:** [September 10, 2024, 8:47am UTC](https://help.galaxyproject.org/t/optimizing-star-mapping-for-large-scale-genome-annotation-managing-memory-overflows-in-rna-seq-workflows/13319 "2024-09-10T08:47:28Z")
I am currently working on annotating a new genome. The genome of this crop is extremely large, ranging from 15G to 18G. My approach is to align RNA-seq data from multiple samples to this genome, then input the BAM fil… --- ## [qiime2 feature-classifier fit-classifier-naive-bayes](https://help.galaxyproject.org/t/qiime2-feature-classifier-fit-classifier-naive-bayes/13395)
**Author:** [@marisaguido](https://help.galaxyproject.org/u/marisaguido)\ **Replies:** 1\ **Last updated:** [September 9, 2024, 5:24pm UTC](https://help.galaxyproject.org/t/qiime2-feature-classifier-fit-classifier-naive-bayes/13395 "2024-09-09T17:24:12Z")
Hi! I have been trying to run this command but it keeps failing with the error of “This tool was terminated because it used more memory than it was allocated”. However, this is the first time I’ve used galaxy and I have … --- ## [MACS2 bdgcmp troubleshooting](https://help.galaxyproject.org/t/macs2-bdgcmp-troubleshooting/13324)
**Author:** [@TTP](https://help.galaxyproject.org/u/TTP)\ **Replies:** 4\ **Last updated:** [August 28, 2024, 11:35pm UTC](https://help.galaxyproject.org/t/macs2-bdgcmp-troubleshooting/13324 "2024-08-28T23:35:17Z")
Hi- I am wondering again if there is some way around these memory use errors I keep getting. This one is with MACS2 bdgcmp. Is it possible to increase the allocation for this tool? --- ## [MAF to FASTA times out](https://help.galaxyproject.org/t/maf-to-fasta-times-out/13247)
**Author:** [@Alasdair\_T](https://help.galaxyproject.org/u/Alasdair_T)\ **Replies:** 3\ **Last updated:** [August 27, 2024, 8:30pm UTC](https://help.galaxyproject.org/t/maf-to-fasta-times-out/13247 "2024-08-27T20:30:04Z")
Hi, I’ve successfully used MAF to FASTA a few times on a ~400Mb MAF file using the one species per line setting, it’s incredibly convenient! However, it is now being terminated due to exceeding the maximum run time wit… --- ## [This job was terminated because it used more memory than it was allocated](https://help.galaxyproject.org/t/this-job-was-terminated-because-it-used-more-memory-than-it-was-allocated/13008)
**Author:** [@Rose](https://help.galaxyproject.org/u/Rose)\ **Replies:** 2\ **Last updated:** [July 22, 2024, 3:08pm UTC](https://help.galaxyproject.org/t/this-job-was-terminated-because-it-used-more-memory-than-it-was-allocated/13008 "2024-07-22T15:08:10Z")
Hi. I’m trying to use this tool but as the error says the tool run out of memory. I think that the problem is not in the input dataset (bam). Overall the workflow I’m trying to follow IS heavy since it works with WXS da… --- ## [ram allocation for reference genome in STAR](https://help.galaxyproject.org/t/ram-allocation-for-reference-genome-in-star/12589)
**Author:** [@RUBA\_DEVI](https://help.galaxyproject.org/u/RUBA_DEVI)\ **Replies:** 1\ **Last updated:** [May 28, 2024, 8:02pm UTC](https://help.galaxyproject.org/t/ram-allocation-for-reference-genome-in-star/12589 "2024-05-28T20:02:49Z")
EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=59392000000is too small for your genome SOLUTION: please specify --limitGenomeGenerateRAM not less than 102018755509 and make that much RAM available May… --- ## [bbtools:bbduk memory issue](https://help.galaxyproject.org/t/bbtools-bbduk-memory-issue/12211)
**Author:** [@bethp](https://help.galaxyproject.org/u/bethp)\ **Replies:** 4\ **Last updated:** [May 23, 2024, 6:50pm UTC](https://help.galaxyproject.org/t/bbtools-bbduk-memory-issue/12211 "2024-05-23T18:50:43Z")
I am trying to use bbtools:bbduk to remove host (mouse) contaminants from my metagenomics data but am running into an issue regarding memory needed for Galaxy to run this, and the job will not complete. Is there a way to… --- ## [Flye crashed with out of memory error](https://help.galaxyproject.org/t/flye-crashed-with-out-of-memory-error/12472)
**Author:** [@chrisbioinfo](https://help.galaxyproject.org/u/chrisbioinfo)\ **Replies:** 3\ **Last updated:** [May 13, 2024, 3:49pm UTC](https://help.galaxyproject.org/t/flye-crashed-with-out-of-memory-error/12472 "2024-05-13T15:49:51Z")
Hello, I was trying to assemble some ONT data with flye, and the job crashed with what looks like out of memory errors based on the logs. Can you set memory limits for jobs in Galaxy? Im attaching the history here for … [Next page](https://help.galaxyproject.org/tag/exceeds-memory-error/385.md?match_all_tags=true&page=1&tags%5B%5D=exceeds-memory-error)