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  • vidjilvidjil
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  • #4030
Closed
Open
Created Oct 31, 2019 by Thonier Florian@flothoniOwner

preprocess; afficher le log si echec

Aujourd'hui un preprocess pear à échoué à cause d'une erreur de format fastq.gz probablement tronqué ou mal généré. En attendant, l'utilisateur ne voit qu'un message d'erreur un peu vague de notre serveur et pas le log de pear. Or celui-ci permet de connaître l'erreur de format (patient 34556).

[ERROR] - Cannot determine the file type of /mnt/upload/uploads/sequence_file.data_file.a1f59a109c47132d.41444e3435302d32305f53325f52325f3030312e66617374712e677a.gz. Ensure it is a BZIP2/GZIP compressed FASTQ file or plain FASTQ.
[...]
PEAR v0.9.10 [May 30, 2016]

Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593

Forward reads file.................: /mnt/upload/uploads/sequence_file.data_file.xxx.gz
Reverse reads file.................: /mnt/upload/uploads/sequence_file.data_file.xxx.gz
PHRED..............................: 33
[...]

Traceback (most recent call last):
  File "pear.py", line 38, in <module>
    raise EnvironmentError("Pear failed")
EnvironmentError: Pear failed

et Affiché: Pb_Vidjil

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