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J'ai un soucis en lançant le pipeline à la première étape (je n'ai pas essayé les étapes suivantes).

L'assemblage se fait correctement, mais ça ne fonctionne plus à l'étape oblisplit. Voici le log du nohup:

[Thu Aug  6 08:44:25 2020]
rule split_sequences:
    input: 03-assign_sequences/180531_SN1126_A_L001_AIMI-18.ali.assigned.fastq
    log: ../99-log/01-assembly/04-split_sequences/180531_SN1126_A_L001_AIMI-18.log
    jobid: 4
    wildcards: run=180531_SN1126_A_L001_AIMI-18

[Thu Aug  6 08:44:25 2020]
Error in rule split_sequences:
    jobid: 4
    log: ../99-log/01-assembly/04-split_sequences/180531_SN1126_A_L001_AIMI-18.log (check log file(s) for error message)
    shell:
        mkdir -p ../02-demultiplex/01-raw/180531_SN1126_A_L001_AIMI-18/; obisplit -p "../02-demultiplex/01-raw/180531_SN1126_A_L001_AIMI-18/" -t sample --fasta 03-assign_sequences/180531_SN1126_A_L001_AIMI-18.ali.assigned.fastq 2> ../99-log/01-assembly/04-split_sequences/180531_SN1126_A_L001_AIMI-18.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /media/superdisk/edna/working/med_sea/snakemake_only_obitools/01-assembly/.snakemake/log/2020-08-05T101334.148600.snakemake.log

Et le log de la commande:

vi ../99-log/01-assembly/04-split_sequences/180531_SN1126_A_L001_AIMI-18.log"

/bin/bash: obisplit: command not found

Donc surement un soucis au niveau de l'accessibilité de cette commande via l'environnement conda?