# Troubleshooting an error (exit code 1) when performing BWA-MEM2 on WGS data **URL:** \ **Category:** usegalaxy.org support\ **Tags:** troubleshooting\ **Created:** [July 28, 2022, 2:48pm UTC](https://help.galaxyproject.org/t/troubleshooting-an-error-exit-code-1-when-performing-bwa-mem2-on-wgs-data/8387 "2022-07-28T14:48:20Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![edf393](https://avatars.discourse-cdn.com/v4/letter/e/bbce88/32.png) [@edf393](https://help.galaxyproject.org/u/edf393)\ **Post date:** [July 28, 2022, 2:48pm UTC](https://help.galaxyproject.org/t/troubleshooting-an-error-exit-code-1-when-performing-bwa-mem2-on-wgs-data/8387/1 "2022-07-28T14:48:20Z")
Hello, I attempted to input two WGS data sets (two different sets of reads) and a reference genome from NCBI into the BWA-MEM2 tool. The job failed and resulting in the following messages: Execution resulted in the following messages: _Fatal error: Exit code 1 ()_ Tool generated the following standard error: _Looking to launch executable “/usr/local/bin/bwa-mem2.avx2”, simd = .avx2_ _Launching executable “/usr/local/bin/bwa-mem2.avx2”_ _[bwa\_index] Pack FASTA… 22.12 sec_ \*\* Entering FMI\_search\* _init ticks = 173525096758_ _ref seq len = 5422419662_ _binary seq ticks = 119852397722_ _Allocation of 40.40 GB for suffix\_array failed._ _Current Allocation = 45.45 GB_ If it helps troubleshoot this issue, I have included some information about the job and the parameters used below. ---
**Author:** ![edf393](https://avatars.discourse-cdn.com/v4/letter/e/bbce88/32.png) [@edf393](https://help.galaxyproject.org/u/edf393)\ **Post date:** [July 28, 2022, 2:50pm UTC](https://help.galaxyproject.org/t/troubleshooting-an-error-exit-code-1-when-performing-bwa-mem2-on-wgs-data/8387/2 "2022-07-28T14:50:12Z")
BWA-MEM2 on data 1, data 8, and data 5 (mapped reads in BAM format) Dbkey: bosTau9 Format: bam Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/bwa\_mem2/bwa\_mem2/2.2.1+galaxy0 Tool Parameters _Will you select a reference genome from your history or use a built-in index?_ History _Use the following dataset as the reference sequence_ Data 5: fasta.gz, 1957 sequences, 801.4 MB, bosTau9 _Single or Paired-end reads_ Paired _Select first set of reads_ Data 8: fastqsanger.gz, 25.2GB, bosTau9 _Select second set of reads_ Data 1: fastqsanger.gz, 25.7 GB, bosTau9 _Enter mean, standard deviation, max, and min for insert lengths._ 150 _Set read groups information?_ Do not set _Select analysis mode_ Illumina _BAM sorting mode_ Sort by chromosomal coordinates _Job Resource Parameters_ No Job Metrics Cores Allocated: 10 Memory Allocated (MB) 29995 Job Runtime (Wall Clock): 6 minutes meminfo Total System Memory: 28.6 GB Total System Swap: 0 bytes ---
**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:** [July 29, 2022, 7:05pm UTC](https://help.galaxyproject.org/t/troubleshooting-an-error-exit-code-1-when-performing-bwa-mem2-on-wgs-data/8387/3 "2022-07-29T19:05:14Z")
Hi @edf393 The FAQs explain what you can do in general to continue working at a public Galaxy server. In short: use an indexed genome as the mapping target (`bosTau8` instead) + split the query reads into a collection, run some QA, map, then merge the results. Or, you can consider setting up a private Galaxy server with scaled up resources. Details: - The job failed for exceeding memory limits at the public Galaxy server [FAQ](https://training.galaxyproject.org/training-material/faqs/galaxy/#understanding-exceeds-memory-allocation-error-messages). - Specifically: - The fastq datasets are too large – ~25 GB compressed per end. [FAQ](https://training.galaxyproject.org/training-material/faqs/galaxy/#working-with-very-large-fastq-datasets) - The fasta custom genome is too large, plus has a formatting problem. [FAQ](https://training.galaxyproject.org/training-material/faqs/galaxy/#working-with-very-large-fasta-datasets) ---
**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:** [September 20, 2023, 9:00pm UTC](https://help.galaxyproject.org/t/troubleshooting-an-error-exit-code-1-when-performing-bwa-mem2-on-wgs-data/8387/4 "2023-09-20T21:00:19Z")
A post was split to a new topic: [Troubleshooting BWA-MEM2 resources under Docker Galaxy](https://help.galaxyproject.org/t/troubleshooting-bwa-mem2-resources-under-docker-galaxy/10819) ---
**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:** [September 20, 2023, 9:00pm UTC](https://help.galaxyproject.org/t/troubleshooting-an-error-exit-code-1-when-performing-bwa-mem2-on-wgs-data/8387/5 "2023-09-20T21:00:26Z")