MSA generation tool
Job name: DHS-ERK2 complex
Job progress history
None
host: node07
Building DAG of jobs...
You are running snakemake in a SLURM job context. This is not recommended, as it may lead to unexpected behavior. Please run Snakemake directly on the login node.
SLURM run ID: 2c5a1975-f46b-4277-941c-ad9b336b8198
Using shell: /usr/bin/bash
Provided remote nodes: 4
Job stats:
job count
----------------- -------
all 1
check_msa 1
check_renamed_msa 1
generate_msa 1
rename_output 1
run_mmseqs 1
setup_db 1
total 7
Select jobs to execute...
Execute 1 jobs...
[Tue Jan 6 11:40:27 2026] Group job msa_generation (jobs in lexicogr. order):
[Tue Jan 6 11:40:27 2026]
Job 5: Running mmseqs2 on /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/query.fasta
Reason: Missing output files: <TBD>; Input files updated by another job: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/LOAD_DB.done
Shell command:
# run colabfold_search
colabfold_search /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/query.fasta uniref30_2202_db /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/mmseqs --db1 /database/db/uniref30_2202/uniref30_2202_db --db-load-mode 2 --db2 . --db3 colabfold_envdb_202108_db --max-accept 1000000 --use-env 0 --use-templates 0 -s 8 --filter 1 --expand-eval inf --align-eval 10 --diff 3000 --qsc 20.0 --mmseqs /opt/MMseqs2/build/bin/mmseqs --threads 1
DAG of jobs will be updated after completion.
[Tue Jan 6 11:40:27 2026]
Job 6: Making sure mmseqs DBs are loaded
Reason: Missing output files: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/LOAD_DB.done
Shell command:
env
### load database into mem if not already and clear any other dbs
# check for previous DBs
DB="/database/db/uniref30_2202/uniref30_2202_db.idx"
ISVM=$(ps aux | grep vm | grep -v grep | wc -l)
if [[ $ISVM -eq 1 ]]; then
# a DB is loaded, check if it's the right one
ISDB=$(ps aux | grep $DB | grep -v grep | wc -l)
if [[ $ISDB -eq 0 ]]; then
# the wrong DB is in cache, it needs to be unloaded first
OLDDB=$(ps aux | grep vm | grep -v grep | awk '{print $NF}')
sudo /usr/local/bin/mmseqs_unload -f $OLDDB
fi
fi
# load the DB
sudo /usr/local/bin/mmseqs_load -f $DB > /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/LOAD_DB.done
No SLURM account given, trying to guess.
Unable to guess SLURM account. Trying to proceed without.
Job 6936c3eb-53b1-5a84-8729-a3acbdb30267 has been submitted with SLURM jobid 426114 (log: slurm-logs/group_msa_generation_run_mmseqs_setup_db/426114.log).
[Tue Jan 6 11:45:33 2026]
Finished jobid: 6 (Rule: setup_db)
[Tue Jan 6 11:45:33 2026]
Finished jobid: 5 (Rule: run_mmseqs)
2 of 7 steps (29%) done
Updating checkpoint dependencies.
Select jobs to execute...
Execute 1 jobs...
[Tue Jan 6 11:45:33 2026]
localrule check_msa:
input: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/mmseqs/0.a3m
output: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/CHECK_MSA.done, /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/msa_list.txt
jobid: 4
reason: Missing output files: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/msa_list.txt
resources: mem_mb=2000, mem_mib=1908, disk_mb=1000, disk_mib=954, tmpdir=/tmp, runtime=30
Shell command: None
Touching output file /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/CHECK_MSA.done.
[Tue Jan 6 11:45:33 2026]
Finished jobid: 4 (Rule: check_msa)
3 of 7 steps (43%) done
Select jobs to execute...
Execute 1 jobs...
[Tue Jan 6 11:45:33 2026]
Job 3: Renaming mmseqs2 outputs
Reason: Missing output files: <TBD>; Input files updated by another job: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/msa_list.txt
Shell command: None
DAG of jobs will be updated after completion.
[Tue Jan 6 11:45:33 2026]
Finished jobid: 3 (Rule: rename_output)
4 of 7 steps (57%) done
Updating checkpoint dependencies.
Select jobs to execute...
Execute 1 jobs...
[Tue Jan 6 11:45:33 2026]
localrule check_renamed_msa:
input: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/renamed_msas/query.a3m
output: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/CHECK_RENAMED_MSA.done, /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/renamed_msa_list.txt
jobid: 2
reason: Missing output files: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/renamed_msa_list.txt
resources: mem_mb=2000, mem_mib=1908, disk_mb=1000, disk_mib=954, tmpdir=/tmp, runtime=30
Shell command: None
Touching output file /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/CHECK_RENAMED_MSA.done.
[Tue Jan 6 11:45:33 2026]
Finished jobid: 2 (Rule: check_renamed_msa)
5 of 7 steps (71%) done
Select jobs to execute...
Execute 1 jobs...
[Tue Jan 6 11:45:33 2026]
localrule generate_msa:
input: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/renamed_msa_list.txt
output: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/query.a3m
jobid: 1
reason: Missing output files: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/query.a3m; Input files updated by another job: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/output/renamed_msa_list.txt
resources: mem_mb=2000, mem_mib=1908, disk_mb=1000, disk_mib=954, tmpdir=/tmp, runtime=30
Shell command: None
[Tue Jan 6 11:45:34 2026]
Finished jobid: 1 (Rule: generate_msa)
6 of 7 steps (86%) done
Select jobs to execute...
Execute 1 jobs...
[Tue Jan 6 11:45:34 2026]
localrule all:
input: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/query.a3m
jobid: 0
reason: Input files updated by another job: /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/query.a3m
resources: mem_mb=2000, mem_mib=1908, disk_mb=1000, disk_mib=954, tmpdir=/tmp, runtime=30
Shell command: None
[Tue Jan 6 11:45:34 2026]
Finished jobid: 0 (Rule: all)
7 of 7 steps (100%) done
Complete log(s): /store/plateformes/BIOI2/webservices/msa_tools/jobs/97c750d2-cfc3-4d33-a946-71a868072d94/.snakemake/log/2026-01-06T114022.688641.snakemake.log