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{foss-2025b} bam-readcount, Clustal-Omega, hifiasm, Pysam - #1923

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Micket wants to merge 3 commits into
EESSI:mainfrom
Micket:bioinfo5
Open

{foss-2025b} bam-readcount, Clustal-Omega, hifiasm, Pysam#1923
Micket wants to merge 3 commits into
EESSI:mainfrom
Micket:bioinfo5

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@Micket

@Micket Micket commented Nov 6, 2026

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Continuing my goal of adding all the requested bioinfo tooling

@ocaisa

ocaisa commented Nov 6, 2026

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bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen3
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen4
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-aws-eu-south for:arch=x86_64/amd/zen5
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/intel/skylake_avx512
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/intel/haswell
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/intel/icelake
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/intel/cascadelake
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/intel/sapphirerapids
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/generic
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=aarch64/generic
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=aarch64/neoverse_n1
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=aarch64/neoverse_v1
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-deucalion for:arch=aarch64/a64fx
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-jsc for:arch=aarch64/nvidia/grace

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen2
Building for: x86_64/amd/zen2
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224857

date job status comment
Nov 06 17:43:39 UTC 2026 submitted job id 224857 awaits release by job manager
Nov 06 17:44:12 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:50:30 UTC 2026 running job 224857 is running
Nov 06 18:23:28 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224857.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17939891920.tar.zstsize: 4 MiB (4297535 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/amd/zen2/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181815UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181732UTC
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
Nov 06 18:23:28 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224857.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen3
Building for: x86_64/amd/zen3
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224858

date job status comment
Nov 06 17:43:44 UTC 2026 submitted job id 224858 awaits release by job manager
Nov 06 17:44:15 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:52:00 UTC 2026 running job 224858 is running
Nov 06 18:18:59 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224858.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen3-17939889580.tar.zstsize: 4 MiB (4298761 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/amd/zen3/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/amd/zen3/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/amd/zen3/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181434UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181402UTC
other under 2025.06/software/linux/x86_64/amd/zen3
no other files in tarball
Nov 06 18:18:59 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224858.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws-eu-south

eessi-bot-aws-eu-south Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-aws-eu-south for repository eessi.io-2025.06-software
Building on: amd-zen5
Building for: x86_64/amd/zen5
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/701

date job status comment
Nov 06 17:43:45 UTC 2026 submitted job id 701 awaits release by job manager
Nov 06 17:44:43 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:51:25 UTC 2026 running job 701 is running
Nov 06 18:07:41 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-701.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen5-17939883210.tar.zstsize: 4 MiB (4295003 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/amd/zen5/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/amd/zen5/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/amd/zen5/reprod
argtable/2.13-GCCcore-14.3.0/20261106_180435UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_180415UTC
other under 2025.06/software/linux/x86_64/amd/zen5
no other files in tarball
Nov 06 18:07:41 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-701.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: amd-zen4
Building for: x86_64/amd/zen4
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224859

date job status comment
Nov 06 17:43:49 UTC 2026 submitted job id 224859 awaits release by job manager
Nov 06 17:44:17 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:53:33 UTC 2026 running job 224859 is running
Nov 06 18:17:25 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224859.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen4-17939887750.tar.zstsize: 4 MiB (4295890 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/amd/zen4/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/amd/zen4/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/amd/zen4/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181150UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181123UTC
other under 2025.06/software/linux/x86_64/amd/zen4
no other files in tarball
Nov 06 18:17:25 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224859.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-deucalion

eessi-bot-deucalion Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-deucalion for repository eessi.io-2025.06-software
Building on: a64fx
Building for: aarch64/a64fx
Job dir: /home/eessibot/new-bot/jobs/2026.11/pr_1923/2202664

date job status comment
Nov 06 17:43:53 UTC 2026 submitted job id 2202664 awaits release by job manager
Nov 06 17:44:00 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:45:10 UTC 2026 running job 2202664 is running
Nov 06 18:44:08 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-2202664.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-a64fx-17939902860.tar.zstsize: 4 MiB (4837700 bytes)
entries: 107
modules under 2025.06/software/linux/aarch64/a64fx/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/a64fx/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/a64fx/reprod
argtable/2.13-GCCcore-14.3.0/20261106_183229UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_183116UTC
other under 2025.06/software/linux/aarch64/a64fx
no other files in tarball
Nov 06 18:44:08 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-2202664.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: intel-skylake_avx512
Building for: x86_64/intel/skylake_avx512
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224860

date job status comment
Nov 06 17:43:56 UTC 2026 submitted job id 224860 awaits release by job manager
Nov 06 17:44:25 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:56:52 UTC 2026 running job 224860 is running
Nov 06 18:15:46 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224860.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-intel-skylake_avx512-17939886830.tar.zstsize: 4 MiB (4654347 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/intel/skylake_avx512/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/intel/skylake_avx512/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/intel/skylake_avx512/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181017UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_180950UTC
other under 2025.06/software/linux/x86_64/intel/skylake_avx512
no other files in tarball
Nov 06 18:15:46 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224860.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-jsc

eessi-bot-jsc Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-jsc for repository eessi.io-2025.06-software
Building on: nvidia-grace
Building for: aarch64/nvidia/grace
Job dir: /p/project1/ceasybuilders/eessibot/jobs/2026.11/pr_1923/15801475

date job status comment
Nov 06 17:44:00 UTC 2026 submitted job id 15801475 awaits release by job manager
Nov 06 17:45:06 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:46:13 UTC 2026 running job 15801475 is running
Nov 06 18:03:44 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-15801475.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-nvidia-grace-17939878810.tar.gzsize: 5 MiB (5375382 bytes)
entries: 107
modules under 2025.06/software/linux/aarch64/nvidia/grace/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/nvidia/grace/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/nvidia/grace/reprod
argtable/2.13-GCCcore-14.3.0/20261106_175645UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_175622UTC
other under 2025.06/software/linux/aarch64/nvidia/grace
no other files in tarball
Nov 06 18:03:44 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-15801475.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: intel-haswell
Building for: x86_64/intel/haswell
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224861

date job status comment
Nov 06 17:44:01 UTC 2026 submitted job id 224861 awaits release by job manager
Nov 06 17:44:20 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:55:10 UTC 2026 running job 224861 is running
Nov 06 18:20:32 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224861.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-intel-haswell-17939889800.tar.zstsize: 4 MiB (4655802 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/intel/haswell/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/intel/haswell/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/intel/haswell/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181452UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181421UTC
other under 2025.06/software/linux/x86_64/intel/haswell
no other files in tarball
Nov 06 18:20:32 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224861.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: intel-icelake
Building for: x86_64/intel/icelake
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224862

date job status comment
Nov 06 17:44:06 UTC 2026 submitted job id 224862 awaits release by job manager
Nov 06 17:44:23 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:55:15 UTC 2026 running job 224862 is running
Nov 06 18:15:43 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224862.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-intel-icelake-17939887970.tar.zstsize: 4 MiB (4653101 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/intel/icelake/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/intel/icelake/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/intel/icelake/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181204UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181140UTC
other under 2025.06/software/linux/x86_64/intel/icelake
no other files in tarball
Nov 06 18:15:43 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224862.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: intel-cascadelake
Building for: x86_64/intel/cascadelake
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224863

date job status comment
Nov 06 17:44:12 UTC 2026 submitted job id 224863 awaits release by job manager
Nov 06 17:46:02 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 18:03:34 UTC 2026 running job 224863 is running
Nov 06 18:23:30 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224863.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-intel-cascadelake-17939891310.tar.zstsize: 4 MiB (4652083 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/intel/cascadelake/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/intel/cascadelake/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/intel/cascadelake/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181736UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181707UTC
other under 2025.06/software/linux/x86_64/intel/cascadelake
no other files in tarball
Nov 06 18:23:30 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224863.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: intel-sapphirerapids
Building for: x86_64/intel/sapphirerapids
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224864

date job status comment
Nov 06 17:44:17 UTC 2026 submitted job id 224864 awaits release by job manager
Nov 06 17:46:05 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 18:05:30 UTC 2026 running job 224864 is running
Nov 06 18:37:51 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224864.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-intel-sapphirerapids-17939899500.tar.zstsize: 4 MiB (4655698 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/intel/sapphirerapids/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/intel/sapphirerapids/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/intel/sapphirerapids/reprod
argtable/2.13-GCCcore-14.3.0/20261106_183125UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_183043UTC
other under 2025.06/software/linux/x86_64/intel/sapphirerapids
no other files in tarball
Nov 06 18:37:51 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224864.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224865

date job status comment
Nov 06 17:44:23 UTC 2026 submitted job id 224865 awaits release by job manager
Nov 06 17:45:59 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 18:01:47 UTC 2026 running job 224865 is running
Nov 06 18:19:01 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224865.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-generic-17939890140.tar.zstsize: 4 MiB (4296841 bytes)
entries: 107
modules under 2025.06/software/linux/x86_64/generic/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/x86_64/generic/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/x86_64/generic/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181542UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181514UTC
other under 2025.06/software/linux/x86_64/generic
no other files in tarball
Nov 06 18:19:01 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224865.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: generic
Building for: aarch64/generic
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224866

date job status comment
Nov 06 17:44:28 UTC 2026 submitted job id 224866 awaits release by job manager
Nov 06 17:45:51 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:59:36 UTC 2026 running job 224866 is running
Nov 06 18:17:22 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224866.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-generic-17939887300.tar.zstsize: 4 MiB (4626922 bytes)
entries: 107
modules under 2025.06/software/linux/aarch64/generic/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/generic/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/generic/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181101UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181038UTC
other under 2025.06/software/linux/aarch64/generic
no other files in tarball
Nov 06 18:17:22 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224866.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: neoverse_n1
Building for: aarch64/neoverse_n1
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224867

date job status comment
Nov 06 17:44:33 UTC 2026 submitted job id 224867 awaits release by job manager
Nov 06 17:45:54 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:59:43 UTC 2026 running job 224867 is running
Nov 06 18:15:41 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224867.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-neoverse_n1-17939887700.tar.zstsize: 4 MiB (4630122 bytes)
entries: 107
modules under 2025.06/software/linux/aarch64/neoverse_n1/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/neoverse_n1/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/neoverse_n1/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181142UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181118UTC
other under 2025.06/software/linux/aarch64/neoverse_n1
no other files in tarball
Nov 06 18:15:41 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224867.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-aws

eessi-bot-aws Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-software
Building on: neoverse_v1
Building for: aarch64/neoverse_v1
Job dir: /project/def-users/SHARED/jobs/2026.11/pr_1923/224868

date job status comment
Nov 06 17:44:38 UTC 2026 submitted job id 224868 awaits release by job manager
Nov 06 17:45:57 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 17:59:49 UTC 2026 running job 224868 is running
Nov 06 18:18:57 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-224868.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-neoverse_v1-17939889920.tar.zstsize: 4 MiB (4634351 bytes)
entries: 107
modules under 2025.06/software/linux/aarch64/neoverse_v1/modules/all
argtable/2.13-GCCcore-14.3.0.lua
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/neoverse_v1/software
argtable/2.13-GCCcore-14.3.0
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/neoverse_v1/reprod
argtable/2.13-GCCcore-14.3.0/20261106_181524UTC
bam-readcount/1.0.1-GCC-14.3.0/20261106_181501UTC
other under 2025.06/software/linux/aarch64/neoverse_v1
no other files in tarball
Nov 06 18:18:57 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-224868.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@casparvl

casparvl commented Nov 6, 2026

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FYI: from the logs:

ERROR: Installation of Clustal-Omega-1.2.4-GCC-14.3.0.eb failed: Couldn't find file clustal-omega-1.2.4.tar.gz anywhere, and downloading it didn't work either...

@Micket

Micket commented Nov 6, 2026

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Hm, homepage is dead, can't find alternatives. Giving up on it.

@ocaisa

ocaisa commented Nov 6, 2026

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bot: build repo:eessi.io-2025.06-software instance:eessi-bot-deucalion for:arch=aarch64/a64fx
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-jsc for:arch=aarch64/nvidia/grace

@eessi-bot-deucalion

eessi-bot-deucalion Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-deucalion for repository eessi.io-2025.06-software
Building on: a64fx
Building for: aarch64/a64fx
Job dir: /home/eessibot/new-bot/jobs/2026.11/pr_1923/2203369

date job status comment
Nov 06 19:30:49 UTC 2026 submitted job id 2203369 awaits release by job manager
Nov 06 19:31:23 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 19:32:29 UTC 2026 running job 2203369 is running
Nov 06 20:25:47 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-2203369.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-a64fx-17939964460.tar.zstsize: 2 MiB (2116621 bytes)
entries: 33
modules under 2025.06/software/linux/aarch64/a64fx/modules/all
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/a64fx/software
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/a64fx/reprod
bam-readcount/1.0.1-GCC-14.3.0/20261106_201449UTC
other under 2025.06/software/linux/aarch64/a64fx
no other files in tarball
Nov 06 20:25:47 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite produced failures.
ReFrame Summary
[ FAILED ] Ran 6/6 test case(s) from 6 check(s) (6 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-2203369.out
❌ found message matching ERROR:
❌ found message matching [\s*FAILED\s*].*Ran .* test case

@eessi-bot-jsc

eessi-bot-jsc Bot commented Nov 6, 2026 •
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New job on instance eessi-bot-jsc for repository eessi.io-2025.06-software
Building on: nvidia-grace
Building for: aarch64/nvidia/grace
Job dir: /p/project1/ceasybuilders/eessibot/jobs/2026.11/pr_1923/15802604

date job status comment
Nov 06 19:30:49 UTC 2026 submitted job id 15802604 awaits release by job manager
Nov 06 19:30:54 UTC 2026 released job awaits launch by Slurm scheduler
Nov 06 19:32:04 UTC 2026 running job 15802604 is running
Nov 06 19:53:49 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-15802604.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-aarch64-nvidia-grace-17939944660.tar.gzsize: 2 MiB (2188270 bytes)
entries: 33
modules under 2025.06/software/linux/aarch64/nvidia/grace/modules/all
bam-readcount/1.0.1-GCC-14.3.0.lua
software under 2025.06/software/linux/aarch64/nvidia/grace/software
bam-readcount/1.0.1-GCC-14.3.0
reprod directories under 2025.06/software/linux/aarch64/nvidia/grace/reprod
bam-readcount/1.0.1-GCC-14.3.0/20261106_194601UTC
other under 2025.06/software/linux/aarch64/nvidia/grace
no other files in tarball
Nov 06 19:53:49 UTC 2026 test result
😢 FAILURE (click triangle for details)
Reason
EESSI test suite was not run, test step itself failed to execute.
Details
✅ job output file slurm-15802604.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@bedroge

bedroge commented Nov 7, 2026

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Similar errors as before with bwa-mem2, bunch of these:

In file included from Levenshtein_distance.cpp:1:
Levenshtein_distance.h:6:10: fatal error: emmintrin.h: No such file or directory
    6 | #include "emmintrin.h"
      |          ^~~~~~~~~~~~~
compilation terminated.

Looks like this doesn't have Arm support yet, though there is an open PR to add this: chhylp123/hifiasm#931.

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4 participants

@Micket @ocaisa @casparvl @bedroge