# Hail Batch & General Cloud **URL:** https://discuss.hail.is/c/hail-batch-general-cloud-support/17.md [Latest](https://discuss.hail.is/latest.md) · [Categories](https://discuss.hail.is/categories.md) --- ## [About the Hail Batch & General Cloud category](https://discuss.hail.is/t/about-the-hail-batch-general-cloud-category/2173)
**Author:** [@danking](https://discuss.hail.is/u/danking)\ **Replies:** 0
Support for the use of Hail Batch and general use of cloud computing. Hail Batch (docs, UI) is a job scheduler and elastic, cloud cluster manager. --- ## [ABFS (abfs://) paths with ADLS Gen2 no longer work in Hail 0.2.137 due to filesystem validation – is it expected / supported?](https://discuss.hail.is/t/abfs-abfs-paths-with-adls-gen2-no-longer-work-in-hail-0-2-137-due-to-filesystem-validation-is-it-expected-supported/4221)
**Author:** [@souckmi](https://discuss.hail.is/u/souckmi)\ **Replies:** 1\ **Last updated:** [March 11, 2026, 8:18pm UTC](https://discuss.hail.is/t/abfs-abfs-paths-with-adls-gen2-no-longer-work-in-hail-0-2-137-due-to-filesystem-validation-is-it-expected-supported/4221 "2026-03-11T20:18:02Z")
Hi, we recently upgraded our pipeline from an older Hail and ran into an issue when working with Azure Data Lake Storage Gen2 using ABFS (abfs://) paths. Our setup: Hail: 0.2.137 Spark: 3.5.7 Scala: 2.12 Java: 11 Pyt… --- ## [Writing MatrixTable on DNAnexus extremely slow + “server connection failed” at the end](https://discuss.hail.is/t/writing-matrixtable-on-dnanexus-extremely-slow-server-connection-failed-at-the-end/4218)
**Author:** [@marise](https://discuss.hail.is/u/marise)\ **Replies:** 0\ **Last updated:** [November 26, 2025, 2:14pm UTC](https://discuss.hail.is/t/writing-matrixtable-on-dnanexus-extremely-slow-server-connection-failed-at-the-end/4218 "2025-11-26T14:14:32Z")
Hi everyone, I’m working with UK Biobank exome sequences (450k individuals) on DNAnexus using Hail, and I’m having persistent issues when trying to write a MatrixTable. My goal is to create the MatrixTable so I can lat… --- ## [Error running hail 0.2.134-py3.11](https://discuss.hail.is/t/error-running-hail-0-2-134-py3-11/4201)
**Author:** [@Elizabeth\_Kiernan](https://discuss.hail.is/u/Elizabeth_Kiernan)\ **Replies:** 1\ **Last updated:** [October 29, 2025, 7:58pm UTC](https://discuss.hail.is/t/error-running-hail-0-2-134-py3-11/4201 "2025-10-29T19:58:50Z")
Hi Hail team, I’m converting a large VDS to VCF via WDL and hitting what looks like a partioning-related error: Traceback (most recent call last): File “”, line 69, in File “”, line 2, in export\_vcf File “/usr/l… --- ## [Out of memory on hail batch?](https://discuss.hail.is/t/out-of-memory-on-hail-batch/4152)
**Author:** [@Trisha\_Karani](https://discuss.hail.is/u/Trisha_Karani)\ **Replies:** 2\ **Last updated:** [June 23, 2025, 4:31pm UTC](https://discuss.hail.is/t/out-of-memory-on-hail-batch/4152 "2025-06-23T16:31:21Z")
I submitted a hail batch job and I got an out of memory error. I believe I am running on my team’s google cloud account (nnf-karczewski), so not sure how it would run out of memory. \[Stage 2:======\> … --- ## [Running hail on slurm](https://discuss.hail.is/t/running-hail-on-slurm/4097)
**Author:** [@Pinegraphite123](https://discuss.hail.is/u/Pinegraphite123)\ **Replies:** 2\ **Last updated:** [May 21, 2025, 3:07am UTC](https://discuss.hail.is/t/running-hail-on-slurm/4097 "2025-05-21T03:07:07Z")
Hi there, Im trying to do some ancestry stuff after getting vcf from a nextflow pipeline. I used conda kernel to run jupyternotebook on hpc vscode. import os os.environ\["JAVA\_HOME"\] = "/home1/xiesheng/jdk-21.0.6" o… --- ## [Export\_plink method uses /tmp instead of tmp\_dir](https://discuss.hail.is/t/export-plink-method-uses-tmp-instead-of-tmp-dir/4116)
**Author:** [@ktrn](https://discuss.hail.is/u/ktrn)\ **Replies:** 0\ **Last updated:** [April 26, 2025, 9:14pm UTC](https://discuss.hail.is/t/export-plink-method-uses-tmp-instead-of-tmp-dir/4116 "2025-04-26T21:14:06Z")
I am running hail using HPC cluster (using 4 nodes on the MPI queue). I am setting tmp\_dir within hl.init() function: hl.init(log='katia.log', tmp\_dir='/my/path/tmp', spark\_conf={ 'spark.local.d… --- ## [Running Hail using MPI queue](https://discuss.hail.is/t/running-hail-using-mpi-queue/4101)
**Author:** [@ktrn](https://discuss.hail.is/u/ktrn)\ **Replies:** 1\ **Last updated:** [April 8, 2025, 3:59pm UTC](https://discuss.hail.is/t/running-hail-using-mpi-queue/4101 "2025-04-08T15:59:34Z")
Our users run Hail using our HPC MPI queues. We have several MPI queues. One queue with 64 cores per node (each node has 512GB of RAM). We also have an MPI queue with 28 cores per node (each node has 256 GB of memory). … --- ## [Recovering older version in jupyterlab](https://discuss.hail.is/t/recovering-older-version-in-jupyterlab/4055)
**Author:** [@Seayy](https://discuss.hail.is/u/Seayy)\ **Replies:** 0\ **Last updated:** [February 16, 2025, 5:20am UTC](https://discuss.hail.is/t/recovering-older-version-in-jupyterlab/4055 "2025-02-16T05:20:21Z")
I run previous version of hail in jupyterlab with spark on DNAnexus.Usually it exported files within an hour. Howvere, after update, I can’t export my vcf with the new version over 10 hours. I wonder how can I recover … --- ## [LineTooLong Error](https://discuss.hail.is/t/linetoolong-error/4037)
**Author:** [@ehsanali](https://discuss.hail.is/u/ehsanali)\ **Replies:** 2\ **Last updated:** [January 28, 2025, 11:04pm UTC](https://discuss.hail.is/t/linetoolong-error/4037 "2025-01-28T23:04:06Z")
Hello, In All of Us, I am trying to calculate a PRS score with around 40000 SNPs. I used the following code with a 2/30 cluster each with 16 CPUs and 104 Ram. But I get this error: LineTooLong … --- ## [\[ERROR\] An error occurred: HailException: RelationalSetup.writeMetadata: file already exists: output.filtered\_data](https://discuss.hail.is/t/error-an-error-occurred-hailexception-relationalsetup-writemetadata-file-already-exists-output-filtered-data/4025)
**Author:** [@smareedu](https://discuss.hail.is/u/smareedu)\ **Replies:** 0\ **Last updated:** [January 18, 2025, 9:01am UTC](https://discuss.hail.is/t/error-an-error-occurred-hailexception-relationalsetup-writemetadata-file-already-exists-output-filtered-data/4025 "2025-01-18T09:01:36Z")
Here is my code: import hail as hl import logging Configure logger logging.basicConfig(level=logging.INFO, format=“%(asctime)s \[%(levelname)s\] %(message)s”) logger = logging.getLogger(name) def main(): logger.info(… --- ## [Cost estimation strategies](https://discuss.hail.is/t/cost-estimation-strategies/3953)
**Author:** [@kasittig](https://discuss.hail.is/u/kasittig)\ **Replies:** 0\ **Last updated:** [October 3, 2024, 10:07pm UTC](https://discuss.hail.is/t/cost-estimation-strategies/3953 "2024-10-03T22:07:12Z")
Hi all! I’m the new Hail team Engineering Manager, and I’m hoping to improve our resources around estimating compute costs. I’d love to hear about anyone’s experience doing anything related to estimating compute costs … --- ## [Filtering samples from VDS in Google cloud](https://discuss.hail.is/t/filtering-samples-from-vds-in-google-cloud/3718)
**Author:** [@jasmussen](https://discuss.hail.is/u/jasmussen)\ **Replies:** 11\ **Last updated:** [August 6, 2024, 8:44pm UTC](https://discuss.hail.is/t/filtering-samples-from-vds-in-google-cloud/3718 "2024-08-06T20:44:31Z")
Hi – I’m working in the AoU Google cloud environment. I’m trying to subset about 500 samples from the WGS Hail VDS and I’m not sure if I’m completely off the mark here or not. I’ve successfully worked with the WGS Hail M… --- ## [AssertionError: assertion failed](https://discuss.hail.is/t/assertionerror-assertion-failed/3644)
**Author:** [@irun](https://discuss.hail.is/u/irun)\ **Replies:** 2\ **Last updated:** [July 26, 2024, 9:30pm UTC](https://discuss.hail.is/t/assertionerror-assertion-failed/3644 "2024-07-26T21:30:15Z")
Hi! I am trying to generate hail indexes for the imputed bgen files in RAP (dnanexus platform) for UK Biobank data processing. The command bellow has worked fine for all the chromosomes except chromosome 4, for which I … --- ## [No FileSystem for scheme "gs"](https://discuss.hail.is/t/no-filesystem-for-scheme-gs/3885)
**Author:** [@Newbie](https://discuss.hail.is/u/Newbie)\ **Replies:** 2\ **Last updated:** [June 21, 2024, 9:51am UTC](https://discuss.hail.is/t/no-filesystem-for-scheme-gs/3885 "2024-06-21T09:51:02Z")
Hi all, I know that this topic has been raised already several times but I am still facing the issue in the title. I am interested in reading the files from the gnomAD project. Hail version: pip show hail Name: hail… --- ## [Unable to write matrix tables to MinIO S3 storage](https://discuss.hail.is/t/unable-to-write-matrix-tables-to-minio-s3-storage/3789)
**Author:** [@cesco](https://discuss.hail.is/u/cesco)\ **Replies:** 1\ **Last updated:** [March 29, 2024, 6:08pm UTC](https://discuss.hail.is/t/unable-to-write-matrix-tables-to-minio-s3-storage/3789 "2024-03-29T18:08:42Z")
Hi, I’m attempting to set up Hail to both read from and write matrix tables to a MinIO (S3 compatible) storage, but so far I’ve only been successful in reading them. I’m using Spark 3.3.2. I have installed both hadoop-… --- ## [Best practices for setting up GCP billing for Hail for the first time](https://discuss.hail.is/t/best-practices-for-setting-up-gcp-billing-for-hail-for-the-first-time/3765)
**Author:** [@Yuan\_Lian](https://discuss.hail.is/u/Yuan_Lian)\ **Replies:** 1\ **Last updated:** [March 21, 2024, 7:02pm UTC](https://discuss.hail.is/t/best-practices-for-setting-up-gcp-billing-for-hail-for-the-first-time/3765 "2024-03-21T19:02:55Z")
Can you please clarify what is best practice for a new user using Hail with GCP for the first time, how to get billing set up so that we have the ability to use dataproc and requester pays buckets? I am a new Broadie an… --- ## [Slow Terra Output](https://discuss.hail.is/t/slow-terra-output/3750)
**Author:** [@beneopp](https://discuss.hail.is/u/beneopp)\ **Replies:** 2\ **Last updated:** [March 11, 2024, 5:23pm UTC](https://discuss.hail.is/t/slow-terra-output/3750 "2024-03-11T17:23:26Z")
I am trying to use Hail in order to upload 1,000 genomes and HGDP data on Gnomad, remove low-quality variants and samples, and subset the variants to be in my exome data. However, it appears to be slow. I tried using the… --- ## [Most efficiently using cloud resources](https://discuss.hail.is/t/most-efficiently-using-cloud-resources/3756)
**Author:** [@eilidh](https://discuss.hail.is/u/eilidh)\ **Replies:** 3\ **Last updated:** [March 1, 2024, 12:57pm UTC](https://discuss.hail.is/t/most-efficiently-using-cloud-resources/3756 "2024-03-01T12:57:40Z")
Hi there, I’m currently processing pVCF files for 500k exomes using Hail on the UKBB RAP. I’m trying to make this as efficient as possible given the costs of these analyses, and have a question about tasks that appear t… --- ## [Incompatibility between Hail and Spark 3.3.2](https://discuss.hail.is/t/incompatibility-between-hail-and-spark-3-3-2/3616)
**Author:** [@ireneisdoomed](https://discuss.hail.is/u/ireneisdoomed)\ **Replies:** 2\ **Last updated:** [October 18, 2023, 10:47am UTC](https://discuss.hail.is/t/incompatibility-between-hail-and-spark-3-3-2/3616 "2023-10-18T10:47:48Z")
Hi! We are experiencing issues with several pipelines that rely on Hail. We run them on a Dataproc cluster in Google Cloud Platform, and we have observed that after an update to the Dataproc images we keep running into … --- ## [Error in Terra When Initializing HAIL](https://discuss.hail.is/t/error-in-terra-when-initializing-hail/3591)
**Author:** [@beneopp](https://discuss.hail.is/u/beneopp)\ **Replies:** 5\ **Last updated:** [October 4, 2023, 8:11pm UTC](https://discuss.hail.is/t/error-in-terra-when-initializing-hail/3591 "2023-10-04T20:11:35Z")
I was unable to implement the 01-genome-wide-association-study.ipynb notebook on Hail-Notebook-Tutorials. I received the following warning after the hl.init() command: /opt/conda/lib/python3.10/site-packages/hailtop/aio… --- ## [Optimal analysis environment for exporting hail table/matrix table to plink or vcf file format](https://discuss.hail.is/t/optimal-analysis-environment-for-exporting-hail-table-matrix-table-to-plink-or-vcf-file-format/3443)
**Author:** [@arora](https://discuss.hail.is/u/arora)\ **Replies:** 1\ **Last updated:** [June 21, 2023, 9:20pm UTC](https://discuss.hail.is/t/optimal-analysis-environment-for-exporting-hail-table-matrix-table-to-plink-or-vcf-file-format/3443 "2023-06-21T21:20:32Z")
Hi! I wanted to get some insights on the optimal cloud configurations for exporting hail table or hail matrix table? Attached is a screenshot of the cloud analysis environment configuration I can work with. Are there cer… --- ## [GCP jupyter error](https://discuss.hail.is/t/gcp-jupyter-error/3093)
**Author:** [@sk4919](https://discuss.hail.is/u/sk4919)\ **Replies:** 6\ **Last updated:** [February 8, 2023, 1:12pm UTC](https://discuss.hail.is/t/gcp-jupyter-error/3093 "2023-02-08T13:12:26Z")
Hello I’ve updated to the latest version of hail, by running pip uninstall followed by pip-install hail. hail version: 0.2.108-fc03e9d5dc08 I create a cluster using the following command: hailctl dataproc start my-ha… --- ## [I would like to use my Hail Batch service account with Terra. How do I do that?](https://discuss.hail.is/t/i-would-like-to-use-my-hail-batch-service-account-with-terra-how-do-i-do-that/3066)
**Author:** [@danking](https://discuss.hail.is/u/danking)\ **Replies:** 1\ **Last updated:** [January 17, 2023, 10:54pm UTC](https://discuss.hail.is/t/i-would-like-to-use-my-hail-batch-service-account-with-terra-how-do-i-do-that/3066 "2023-01-17T22:54:11Z")
I would like to use the Hail team’s hosted version of Hail Batch (https://batch.hail.is) with datasets stored in Terra. How do I do that? --- ## [Combining VCFs from gnomAD](https://discuss.hail.is/t/combining-vcfs-from-gnomad/2910)
**Author:** [@rye335](https://discuss.hail.is/u/rye335)\ **Replies:** 3\ **Last updated:** [October 21, 2022, 3:28pm UTC](https://discuss.hail.is/t/combining-vcfs-from-gnomad/2910 "2022-10-21T15:28:13Z")
Hi, I’m interested in combining VCFs from gnomAD and was wondering if there’s an efficient way to do this in Hail (for example, parallelizing the operation by chromosome). Thanks! --- ## [Getting java heap error tried a bunch of things with the executor and memory settings](https://discuss.hail.is/t/getting-java-heap-error-tried-a-bunch-of-things-with-the-executor-and-memory-settings/2753)
**Author:** [@jerome-f](https://discuss.hail.is/u/jerome-f)\ **Replies:** 2\ **Last updated:** [October 5, 2022, 3:49am UTC](https://discuss.hail.is/t/getting-java-heap-error-tried-a-bunch-of-things-with-the-executor-and-memory-settings/2753 "2022-10-05T03:49:55Z")
Hi, I am running hail and spark on local linux cluster and using the Pan-UKBB data which comes in hail tables. I am heap errors repeatedly I tried throwing more memory at it increasing the available memory etc. I am run… --- ## [Pip-installed Hail requires additional configuration options in Spark referring to the path to the Hail Python module directory HAIL\_DIR](https://discuss.hail.is/t/pip-installed-hail-requires-additional-configuration-options-in-spark-referring-to-the-path-to-the-hail-python-module-directory-hail-dir/2685)
**Author:** [@bpark](https://discuss.hail.is/u/bpark)\ **Replies:** 1\ **Last updated:** [June 3, 2022, 6:48am UTC](https://discuss.hail.is/t/pip-installed-hail-requires-additional-configuration-options-in-spark-referring-to-the-path-to-the-hail-python-module-directory-hail-dir/2685 "2022-06-03T06:48:05Z")
Hi I build hail 0.2.95, and it is OK. I run pyspark with jupyter notebook hl.init(sc=sc) The message is out this. pip-installed Hail requires additional configuration options in Spark referring to the path to the H… --- ## [Build hail on cloud](https://discuss.hail.is/t/build-hail-on-cloud/2683)
**Author:** [@bpark](https://discuss.hail.is/u/bpark)\ **Replies:** 1\ **Last updated:** [May 28, 2022, 2:12am UTC](https://discuss.hail.is/t/build-hail-on-cloud/2683 "2022-05-28T02:12:50Z")
Hi! The cloud is spark cluster with CentOS 7. I make install-on-cluster HAIL\_COMPILE\_NATIVES=1 SCALA\_VERSION=2.12.13 SPARK\_VERSION=3.1.1 BUILD SUCCESSFUL But sed ‘/^pyspark/d’ python/requirements.txt | grep -v ‘^#’ … --- ## [Best archival policy for storing hail matrix tables in aws s3 bucket](https://discuss.hail.is/t/best-archival-policy-for-storing-hail-matrix-tables-in-aws-s3-bucket/2679)
**Author:** [@Abhishek](https://discuss.hail.is/u/Abhishek)\ **Replies:** 1\ **Last updated:** [May 24, 2022, 2:07pm UTC](https://discuss.hail.is/t/best-archival-policy-for-storing-hail-matrix-tables-in-aws-s3-bucket/2679 "2022-05-24T14:07:27Z")
Hi, Our team is currently working with UKBB releases of 200K and 450K WES. We have created lots of hail matrix tables(initial, preprocessing and analysis stage) and stored them in aws s3 storage in glacier mode(for cost… --- ## [How to get a non-trial Hail Batch Billing Account?](https://discuss.hail.is/t/how-to-get-a-non-trial-hail-batch-billing-account/2668)
**Author:** [@iwong](https://discuss.hail.is/u/iwong)\ **Replies:** 1\ **Last updated:** [May 16, 2022, 10:52pm UTC](https://discuss.hail.is/t/how-to-get-a-non-trial-hail-batch-billing-account/2668 "2022-05-16T22:52:53Z")
I’ve used all the free compute credits from the trial account. I would like to set up a proper billing Batch Billing Project to continue using the system but cannot find any documentation on how to set this up. [Next page](https://discuss.hail.is/c/hail-batch-general-cloud-support/17.md?page=1)