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  • edna
  • snakemake_rapidrun_obitoolssnakemake_rapidrun_obitools
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  • #14
Closed
Open
Created Feb 02, 2022 by vmarques@vmarquesOwner

Error running pipeline

J'ai une erreur en lançant ce pipeline sur un projet en particulier (les autres ont marché)

Le projet complet est là

/media/superdisk/edna/working/lengguru/snakemake_rapidrun_obitools

On dirait que l'erreur initiale provient d'une étape dont voici le log:

vi logs/10_goodlength_samples/Lengguru/teleo/180514_SND405_A_L002_AIMI-14/SPY181026_01.log

results/09_dereplicate_samples/Lengguru/teleo/180514_SND405_A_L002_AIMI-14/SPY181026_01.uniq.fasta   0.0 % |/                                                  ] remain : 00:01:38^Mresults/09_dereplicate_samples/Lengguru/teleo/180514_SND405_A_L002_AIMI-14/SPY181026_01.uniq.fasta   0.0 % |-                                                  ] remain : 00:00:00^Mresults/09_dereplicate_samples/Lengguru/teleo/180514_SND405_A_L002_AIMI-14/SPY181026_01.uniq.fasta   0.0 % |\                                                  ] remain : 00:00:01Traceback (most recent call last):
  File "/media/superdisk/edna/working/lengguru/snakemake_rapidrun_obitools/.snakemake/conda/4d24d54c/bin/obigrep", line 42, in <module>
    for seq in goodSeq(entries):
  File "src/obitools/options/_bioseqfilter.pyx", line 79, in sequenceFilterIterator
  File "src/obitools/options/_bioseqfilter.pyx", line 52, in obitools.options._bioseqfilter.filterGenerator.sequenceFilter
  File "src/obitools/options/_bioseqfilter.pyx", line 53, in genexpr
  File "<string>", line 1, in <module>
NameError: name 'seq_length' is not defined

Et le config exécuté est celui ci, je n'ai rien vu de manquant concernant les paramètres de longueurs de séquence

config/config_lengguru.yaml 
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