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{2025.06}[2024a,2025a,2025b,system] various bioinfo tools#1487

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{2025.06}[2024a,2025a,2025b,system] various bioinfo tools#1487
jpecar wants to merge 2 commits intoEESSI:mainfrom
jpecar:bioinfo_part2

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@jpecar jpecar commented Apr 27, 2026

Some popular bioinformatic tools for 2025.06.

More to come (once I get more comfortable with the whole process).

ocaisa
ocaisa reviewed Apr 27, 2026
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Comment thread easystacks/software.eessi.io/eessi-2025.06-eb-5.2.0-2024a.yml Outdated
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ocaisa commented Apr 27, 2026

bot: build repo:eessi.io-2025.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2

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eessi-bot-aws Bot commented Apr 27, 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/2026.04/pr_1487/151975

date job status comment
Apr 27 14:33:11 UTC 2026 submitted job id 151975 awaits release by job manager
Apr 27 14:33:40 UTC 2026 released job awaits launch by Slurm scheduler
Apr 27 14:39:54 UTC 2026 running job 151975 is running
Apr 27 18:50:17 UTC 2026 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-151975.out
✅ no message matching FATAL:
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.* created!
Artefacts
eessi-2025.06-software-linux-x86_64-amd-zen2-17773155760.tar.zstsize: 1777 MiB (1863904279 bytes)
entries: 58992
modules under 2025.06/software/linux/x86_64/amd/zen2/modules/all
ARAGORN/1.2.41-GCC-14.2.0.lua
BamTools/2.5.3-GCC-14.2.0.lua
barrnap/0.9-gompi-2025a.lua
BBMap/39.19-GCC-14.2.0.lua
BEDTools/2.31.1-GCC-14.2.0.lua
BioPerl/1.7.8-GCCcore-14.2.0.lua
Bio-SearchIO-hmmer/1.7.3-GCC-14.2.0.lua
Bowtie2/2.5.4-GCC-14.3.0.lua
Cbc/2.10.12-foss-2025a.lua
Cgl/0.60.9-foss-2025a.lua
Clp/1.17.10-foss-2025a.lua
CoinUtils/2.11.12-GCC-14.2.0.lua
cutadapt/5.1-GCCcore-13.3.0.lua
cyvcf2/0.32.1-gfbf-2025a.lua
DB/18.1.40-GCCcore-14.2.0.lua
DB_File/1.859-GCCcore-14.2.0.lua
deepTools/3.5.5-gfbf-2024a.lua
DendroPy/5.0.1-GCCcore-13.3.0.lua
DendroPy/5.0.8-GCCcore-14.2.0.lua
fastp/1.1.0-GCC-14.3.0.lua
FastQC/0.12.1-Java-11.lua
FastTree/2.2-GCCcore-14.2.0.lua
GATK/4.6.2.0-GCCcore-14.3.0-Java-17.lua
Ghostscript/10.05.1-GCCcore-14.2.0.lua
GitPython/3.1.45-GCCcore-14.2.0.lua
GLPK/5.0-GCCcore-14.2.0.lua
GMAP-GSNAP/2025-07-31-GCC-14.2.0.lua
HMMER/3.4-gompi-2025a.lua
HMMER/3.4-gompi-2025b.lua
HTSlib/1.22.1-GCC-14.2.0.lua
Infernal/1.1.5-gompi-2025a.lua
IQ-TREE/3.0.1-gompi-2024a.lua
ISA-L/2.31.0-GCCcore-13.3.0.lua
ISA-L/2.31.1-GCCcore-14.3.0.lua
Java/11.0.27.lua
Java/25.36.lua
Java/.modulerc.lua
JsonCpp/1.9.6-GCCcore-14.2.0.lua
k8/1.2-GCCcore-13.3.0.lua
kallisto/0.51.1-gompi-2025a.lua
LSD2/2.4.1-GCCcore-13.3.0.lua
MAFFT/7.526-GCC-14.3.0-with-extensions.lua
MEME/5.5.9-gompi-2025a.lua
MinCED/0.4.2-GCCcore-14.2.0.lua
ncbi-vdb/3.2.1-gompi-2025b.lua
Nextflow/25.10.2.lua
NSPR/4.37-GCCcore-14.3.0.lua
NSS/3.114-GCCcore-14.3.0.lua
Osi/0.108.11-GCC-14.2.0.lua
parallel/20250722-GCCcore-14.2.0.lua
picard/3.4.0-Java-21.lua
pigz/2.8-GCCcore-13.3.0.lua
plotly.py/5.24.1-GCCcore-13.3.0.lua
prodigal/2.6.3-GCCcore-14.2.0.lua
prokka/1.15.6-gompi-2025a.lua
PuLP/3.3.0-foss-2025a.lua
pybedtools/0.12.0-foss-2025a.lua
pyBigWig/0.3.24-gfbf-2024a.lua
pyBigWig/0.3.25-gfbf-2025b.lua
pyfaidx/0.9.0.3-GCCcore-14.3.0.lua
Pysam/0.22.1-GCC-13.3.0.lua
Pysam/0.23.3-GCC-14.2.0.lua
Pysam/0.23.3-GCC-14.3.0.lua
python-isal/1.7.0-GCCcore-13.3.0.lua
RAxML/8.2.13-gompi-2025a.lua
SEPP/4.5.5-foss-2024a.lua
seqtk/1.5-GCC-14.2.0.lua
snakemake/9.14.0-foss-2025a.lua
SPAdes/4.2.0-GCC-14.3.0.lua
table2asn/20250916-GCCcore-14.2.0.lua
Trimmomatic/0.40-Java-17.lua
VCFtools/0.1.17-GCC-14.2.0.lua
versioningit/3.1.2-GCCcore-13.3.0.lua
ViennaRNA/2.7.2-gfbf-2025b.lua
XML-Compile/1.64-GCCcore-14.2.0.lua
XML-LibXML/2.0210-GCCcore-14.2.0.lua
zlib-ng/2.2.1-GCCcore-13.3.0.lua
software under 2025.06/software/linux/x86_64/amd/zen2/software
ARAGORN/1.2.41-GCC-14.2.0
BamTools/2.5.3-GCC-14.2.0
barrnap/0.9-gompi-2025a
BBMap/39.19-GCC-14.2.0
BEDTools/2.31.1-GCC-14.2.0
BioPerl/1.7.8-GCCcore-14.2.0
Bio-SearchIO-hmmer/1.7.3-GCC-14.2.0
Bowtie2/2.5.4-GCC-14.3.0
Cbc/2.10.12-foss-2025a
Cgl/0.60.9-foss-2025a
Clp/1.17.10-foss-2025a
CoinUtils/2.11.12-GCC-14.2.0
cutadapt/5.1-GCCcore-13.3.0
cyvcf2/0.32.1-gfbf-2025a
DB/18.1.40-GCCcore-14.2.0
DB_File/1.859-GCCcore-14.2.0
deepTools/3.5.5-gfbf-2024a
DendroPy/5.0.1-GCCcore-13.3.0
DendroPy/5.0.8-GCCcore-14.2.0
fastp/1.1.0-GCC-14.3.0
FastQC/0.12.1-Java-11
FastTree/2.2-GCCcore-14.2.0
GATK/4.6.2.0-GCCcore-14.3.0-Java-17
Ghostscript/10.05.1-GCCcore-14.2.0
GitPython/3.1.45-GCCcore-14.2.0
GLPK/5.0-GCCcore-14.2.0
GMAP-GSNAP/2025-07-31-GCC-14.2.0
HMMER/3.4-gompi-2025a
HMMER/3.4-gompi-2025b
HTSlib/1.22.1-GCC-14.2.0
Infernal/1.1.5-gompi-2025a
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Java/11.0.27
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k8/1.2-GCCcore-13.3.0
kallisto/0.51.1-gompi-2025a
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MAFFT/7.526-GCC-14.3.0-with-extensions
MEME/5.5.9-gompi-2025a
MinCED/0.4.2-GCCcore-14.2.0
ncbi-vdb/3.2.1-gompi-2025b
Nextflow/25.10.2
NSPR/4.37-GCCcore-14.3.0
NSS/3.114-GCCcore-14.3.0
Osi/0.108.11-GCC-14.2.0
parallel/20250722-GCCcore-14.2.0
picard/3.4.0-Java-21
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prokka/1.15.6-gompi-2025a
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pybedtools/0.12.0-foss-2025a
pyBigWig/0.3.24-gfbf-2024a
pyBigWig/0.3.25-gfbf-2025b
pyfaidx/0.9.0.3-GCCcore-14.3.0
Pysam/0.22.1-GCC-13.3.0
Pysam/0.23.3-GCC-14.2.0
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python-isal/1.7.0-GCCcore-13.3.0
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snakemake/9.14.0-foss-2025a
SPAdes/4.2.0-GCC-14.3.0
table2asn/20250916-GCCcore-14.2.0
Trimmomatic/0.40-Java-17
VCFtools/0.1.17-GCC-14.2.0
versioningit/3.1.2-GCCcore-13.3.0
ViennaRNA/2.7.2-gfbf-2025b
XML-Compile/1.64-GCCcore-14.2.0
XML-LibXML/2.0210-GCCcore-14.2.0
zlib-ng/2.2.1-GCCcore-13.3.0
reprod directories under 2025.06/software/linux/x86_64/amd/zen2/reprod
ARAGORN/1.2.41-GCC-14.2.0/20260427_171638UTC
BamTools/2.5.3-GCC-14.2.0/20260427_163030UTC
barrnap/0.9-gompi-2025a/20260427_171653UTC
BBMap/39.19-GCC-14.2.0/20260427_155008UTC
BEDTools/2.31.1-GCC-14.2.0/20260427_163153UTC
BioPerl/1.7.8-GCCcore-14.2.0/20260427_171555UTC
Bio-SearchIO-hmmer/1.7.3-GCC-14.2.0/20260427_171623UTC
Bowtie2/2.5.4-GCC-14.3.0/20260427_172909UTC
Cbc/2.10.12-foss-2025a/20260427_160918UTC
Cgl/0.60.9-foss-2025a/20260427_160439UTC
Clp/1.17.10-foss-2025a/20260427_155922UTC
CoinUtils/2.11.12-GCC-14.2.0/20260427_155404UTC
cutadapt/5.1-GCCcore-13.3.0/20260427_144654UTC
cyvcf2/0.32.1-gfbf-2025a/20260427_163614UTC
DB/18.1.40-GCCcore-14.2.0/20260427_171450UTC
DB_File/1.859-GCCcore-14.2.0/20260427_171510UTC
deepTools/3.5.5-gfbf-2024a/20260427_145906UTC
DendroPy/5.0.1-GCCcore-13.3.0/20260427_145928UTC
DendroPy/5.0.8-GCCcore-14.2.0/20260427_163636UTC
fastp/1.1.0-GCC-14.3.0/20260427_184455UTC
FastQC/0.12.1-Java-11/20260427_151531UTC
FastTree/2.2-GCCcore-14.2.0/20260427_161957UTC
GATK/4.6.2.0-GCCcore-14.3.0-Java-17/20260427_174524UTC
Ghostscript/10.05.1-GCCcore-14.2.0/20260427_153015UTC
GitPython/3.1.45-GCCcore-14.2.0/20260427_155056UTC
GLPK/5.0-GCCcore-14.2.0/20260427_155218UTC
GMAP-GSNAP/2025-07-31-GCC-14.2.0/20260427_164402UTC
HMMER/3.4-gompi-2025a/20260427_171105UTC
HMMER/3.4-gompi-2025b/20260427_174422UTC
HTSlib/1.22.1-GCC-14.2.0/20260427_163438UTC
Infernal/1.1.5-gompi-2025a/20260427_164855UTC
IQ-TREE/3.0.1-gompi-2024a/20260427_151159UTC
ISA-L/2.31.0-GCCcore-13.3.0/20260427_144516UTC
ISA-L/2.31.1-GCCcore-14.3.0/20260427_184432UTC
Java/11.0.27/20260427_151520UTC
Java/25.36/20260427_151709UTC
JsonCpp/1.9.6-GCCcore-14.2.0/20260427_162944UTC
k8/1.2-GCCcore-13.3.0/20260427_151216UTC
kallisto/0.51.1-gompi-2025a/20260427_165604UTC
LSD2/2.4.1-GCCcore-13.3.0/20260427_150020UTC
MAFFT/7.526-GCC-14.3.0-with-extensions/20260427_174454UTC
MEME/5.5.9-gompi-2025a/20260427_154918UTC
MinCED/0.4.2-GCCcore-14.2.0/20260427_171704UTC
ncbi-vdb/3.2.1-gompi-2025b/20260427_181056UTC
Nextflow/25.10.2/20260427_151725UTC
NSPR/4.37-GCCcore-14.3.0/20260427_182137UTC
NSS/3.114-GCCcore-14.3.0/20260427_184129UTC
Osi/0.108.11-GCC-14.2.0/20260427_155530UTC
parallel/20250722-GCCcore-14.2.0/20260427_171723UTC
picard/3.4.0-Java-21/20260427_151349UTC
pigz/2.8-GCCcore-13.3.0/20260427_144030UTC
plotly.py/5.24.1-GCCcore-13.3.0/20260427_144919UTC
prodigal/2.6.3-GCCcore-14.2.0/20260427_164611UTC
prokka/1.15.6-gompi-2025a/20260427_171840UTC
PuLP/3.3.0-foss-2025a/20260427_160951UTC
pybedtools/0.12.0-foss-2025a/20260427_163305UTC
pyBigWig/0.3.24-gfbf-2024a/20260427_145725UTC
pyBigWig/0.3.25-gfbf-2025b/20260427_184204UTC
pyfaidx/0.9.0.3-GCCcore-14.3.0/20260427_181119UTC
Pysam/0.22.1-GCC-13.3.0/20260427_145650UTC
Pysam/0.23.3-GCC-14.2.0/20260427_162902UTC
Pysam/0.23.3-GCC-14.3.0/20260427_172705UTC
python-isal/1.7.0-GCCcore-13.3.0/20260427_144539UTC
RAxML/8.2.13-gompi-2025a/20260427_162040UTC
SEPP/4.5.5-foss-2024a/20260427_145955UTC
seqtk/1.5-GCC-14.2.0/20260427_163645UTC
snakemake/9.14.0-foss-2025a/20260427_161944UTC
SPAdes/4.2.0-GCC-14.3.0/20260427_182030UTC
table2asn/20250916-GCCcore-14.2.0/20260427_171734UTC
Trimmomatic/0.40-Java-17/20260427_151542UTC
VCFtools/0.1.17-GCC-14.2.0/20260427_163754UTC
versioningit/3.1.2-GCCcore-13.3.0/20260427_144049UTC
ViennaRNA/2.7.2-gfbf-2025b/20260427_180725UTC
XML-Compile/1.64-GCCcore-14.2.0/20260427_153419UTC
XML-LibXML/2.0210-GCCcore-14.2.0/20260427_153337UTC
zlib-ng/2.2.1-GCCcore-13.3.0/20260427_144250UTC
other under 2025.06/software/linux/x86_64/amd/zen2
no other files in tarball
Apr 27 18:50:17 UTC 2026 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ OK ] (1/5) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/22Jul2025-foss-2024a-kokkos %scale=1_node /ade8cad7 @BotBuildTests:x86-64-zen2+default
P: perf: 441.275 timesteps/s (r:0, l:None, u:None)
[ OK ] (2/5) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node %device_type=cpu /e4bf9965 @BotBuildTests:x86-64-zen2+default
P: latency: 1.41 us (r:0, l:None, u:None)
[ OK ] (3/5) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node %device_type=cpu /3da4890b @BotBuildTests:x86-64-zen2+default
P: latency: 2.04 us (r:0, l:None, u:None)
[ OK ] (4/5) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /3255009a @BotBuildTests:x86-64-zen2+default
P: latency: 0.19 us (r:0, l:None, u:None)
[ OK ] (5/5) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /59f4b331 @BotBuildTests:x86-64-zen2+default
P: bandwidth: 7861.14 MB/s (r:0, l:None, u:None)
[ PASSED ] Ran 5/5 test case(s) from 5 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-151975.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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jpecar commented Apr 28, 2026

Will try again one by one

@jpecar jpecar closed this Apr 28, 2026
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@jpecar @ocaisa