MSA-tools

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: 607ec741-31ec-4a4c-a519-4ea2d6e8b979
Using shell: /usr/bin/bash
Provided remote nodes: 4
Job stats:
job                  count
-----------------  -------
all                      1
convert_a3m_fasta        1
total                    2

Select jobs to execute...
Execute 1 jobs...
[Tue Jan  6 11:41:59 2026] Group job convertmsa (jobs in lexicogr. order):
    [Tue Jan  6 11:41:59 2026]
    Job 1: Converting MSA format
    Reason: Missing output files: /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta
Shell command: 
    if [[ /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/query.a3m == *.a3m ]]; then
      firstline=$(head -n 1 /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/query.a3m)
      reformat.pl -r a3m fas /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/query.a3m /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta
      if [[ ${firstline:0:1} == "#" ]] ; then sed -i '1i '"$firstline" /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta ; fi # add the header if there is one
    else
      reformat.pl -r fas a3m /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/query.a3m /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta.tmp.a3m
      # Then make sure you only have 1 line per sequence:
      awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta.tmp.a3m > /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta
      rm /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta.tmp.a3m
    fi
    
No SLURM account given, trying to guess.
Unable to guess SLURM account. Trying to proceed without.
Job 6ef6d60b-4f88-597f-ab7e-a5b3d39745c0 has been submitted with SLURM jobid 426120 (log: slurm-logs/group_convertmsa_convert_a3m_fasta/426120.log).
[Tue Jan  6 11:42:34 2026]
Finished jobid: 1 (Rule: convert_a3m_fasta)
1 of 2 steps (50%) done
Select jobs to execute...
Execute 1 jobs...
[Tue Jan  6 11:42:34 2026]
localrule all:
    input: /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta
    jobid: 0
    reason: Input files updated by another job: /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/output.fasta
    resources: mem_mb=2000, mem_mib=1908, disk_mb=1000, disk_mib=954, tmpdir=/tmp, runtime=30
Shell command: None
[Tue Jan  6 11:42:34 2026]
Finished jobid: 0 (Rule: all)
2 of 2 steps (100%) done
Complete log(s): /store/plateformes/BIOI2/webservices/msa_tools/jobs/55fb9092-4d2f-46ea-a15b-a53c1fcee37e/.snakemake/log/2026-01-06T114154.749130.snakemake.log