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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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singularity install takes >18 hours / freezes #475

Closed tallnuttrbgv closed 4 months ago

tallnuttrbgv commented 4 months ago

There seems to be a problem trying to pull the singularity image.

singularity version 3.11.3

running on HPC with: Linux version 4.18.0-513.24.1.el8.nci.x86_64 (bjmadm@hpc-build.novalocal) (gcc version 8.5.0 20210514 (Red Hat 8.5.0-20) (GCC)) #1 SMP Tue Apr 23 01:46:25 UTC 2024 cat /etc/*-release Rocky Linux release 8.9 (Green Obsidian) NAME="Rocky Linux" VERSION="8.9 (Green Obsidian)" ID="rocky" ID_LIKE="rhel centos fedora" VERSION_ID="8.9" PLATFORM_ID="platform:el8" PRETTY_NAME="Rocky Linux 8.9 (Green Obsidian)" ANSI_COLOR="0;32" LOGO="fedora-logo-icon" CPE_NAME="cpe:/o:rocky:rocky:8:GA" HOME_URL="https://rockylinux.org/" BUG_REPORT_URL="https://bugs.rockylinux.org/" SUPPORT_END="2029-05-31" ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8" ROCKY_SUPPORT_PRODUCT_VERSION="8.9" REDHAT_SUPPORT_PRODUCT="Rocky Linux" REDHAT_SUPPORT_PRODUCT_VERSION="8.9" Rocky Linux release 8.9 (Green Obsidian)

Running command below froze for >18 hours. I have tried several times and it will not complete the pull.

singularity pull EDTA.sif docker://quay.io/biocontainers/edta:1.9.6--1 INFO: Converting OCI blobs to SIF format WARNING: 'nodev' mount option set on /g/data/nm31, it could be a source of failure during build process INFO: Starting build... Getting image source signatures Copying blob dbd31e1d863d done Copying blob cfb1ba34637d done Copying blob 316957f8baaf done Copying blob 75c080ef15eb done Copying blob 1dbcab28ce46 done Copying blob ace2d8a63dd5 done Copying blob 2f8531d5a6ec done Copying blob 1dbcab28ce46 done Copying blob 2e178fd72baf done Copying blob 221e091c5dcb done Copying config e1bcd71354 done Writing manifest to image destination Storing signatures 2024/07/02 18:00:20 info unpack layer: sha256:1dbcab28ce46b65c0174e5e82658492107396fead31e9144c343e6bc96e471c7 2024/07/02 18:00:20 info unpack layer: sha256:cfb1ba34637d96787f6e780192bc5f09c04fe0b40c4e1acdcbc88953bce25b5b 2024/07/02 18:00:20 warn rootless{dev/console} creating empty file in place of device 5:1 2024/07/02 18:07:03 warn xattr{home/default} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2024/07/02 18:07:03 warn xattr{/g/data/nm31/d/tmp/build-temp-559832976/rootfs/home/default} destination filesystem does not support xattrs, further warnings will be suppressed 2024/07/02 18:13:45 info unpack layer: sha256:ace2d8a63dd59063206661355f22da9e1c75c56d6cae5116d91db7a65f640667 2024/07/02 18:13:46 info unpack layer: sha256:75c080ef15ebb28daeadc91eeda0ca95a893fe1f4e55845da3feb58069d42fdc 2024/07/02 18:13:46 info unpack layer: sha256:316957f8baafcefd4c9f72b7e3f3fafb7fcb3ca805dc69d242aef656e0736490 2024/07/02 18:13:46 info unpack layer: sha256:dbd31e1d863d4a41565c08ad1d419c3a3538abfdd4a7971de63b8c5c8a43caec 2024/07/02 18:13:47 info unpack layer: sha256:2f8531d5a6ece34772cf99a2d30e3057c636f1ad05cdec0c8009eab401e616a7 2024/07/02 18:13:47 info unpack layer: sha256:1dbcab28ce46b65c0174e5e82658492107396fead31e9144c343e6bc96e471c7 2024/07/02 18:13:47 info unpack layer: sha256:2e178fd72baf28bc587b5d274574f1a3d3e25ac802fdaf154af258a3c5891831 2024/07/02 18:13:47 info unpack layer: sha256:221e091c5dcbb91400e2b18ccf86cfa9f967ab60b2a28539c98416df1f8740c7

tallnuttrbgv commented 4 months ago

I notice in another comment dev has said only the mamba yml install method works - have now done this on a VM.