Erreur pendant test nextflow

IFB Core Cluster
1

Bonjour,

Je suis en train de tester nextflow sur le cluster.

Pour cela j'essaye de faire tourner le pipeline "test" RNAseq du nf-core.
Je lance la commande :
nextflow run nf-core/rnaseq -profile test,singularity -r 2.0

J'obtiens une erreur m'indiquant que nextflow ne parvient pas à charger une image docker via singularity (ci-dessous), j'ai essayé de créer un fichier nextflow.config contenant "singularity.enabled = true" mais ça n'a pas réglé le problème.

A savoir que quand je lance la commande
singularity pull --name quay.io-biocontainers-subread-2.0.1--hed695b0_0.img.pulling.1611660399320 docker://quay.io/biocontainers/subread:2.0.1--hed695b0_0 > /dev/null
en dehors de nextflow, cela fonctionne bien.

[eb/57ded1] NOTE: Process `RNASEQ:PRESEQ_LCEXTRAP (WT_R2)` terminated with an error exit status (1) -- Error is ignored
Error executing process > 'RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_R1)'

    Caused by:
      Failed to pull singularity image
      command: singularity pull  --name quay.io-biocontainers-subread-2.0.1--hed695b0_0.img.pulling.1611660399320 docker://quay.io/biocontainers/subread:2.0.1--hed695b0_0 > /dev/null
      status : 255
      message:
        time="2021-01-26T12:26:39+01:00" level=warning msg="\"/run/user/100068\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/100068: no such file or directory: Trying to pull image in the event that it is a public image."
        INFO:    Converting OCI blobs to SIF format
        INFO:    Starting build...
        time="2021-01-26T12:26:40+01:00" level=warning msg="\"/run/user/100068\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/100068: no such file or directory: Trying to pull image in the event that it is a public image."
        time="2021-01-26T12:26:41+01:00" level=warning msg="\"/run/user/100068\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/100068: no such file or directory: Trying to pull image in the event that it is a public image."
        Getting image source signatures
        Copying blob sha256:1dbcab28ce46b65c0174e5e82658492107396fead31e9144c343e6bc96e471c7
        Copying blob sha256:cfb1ba34637d96787f6e780192bc5f09c04fe0b40c4e1acdcbc88953bce25b5b
        Copying blob sha256:ace2d8a63dd59063206661355f22da9e1c75c56d6cae5116d91db7a65f640667
        Copying blob sha256:75c080ef15ebb28daeadc91eeda0ca95a893fe1f4e55845da3feb58069d42fdc
        Copying blob sha256:316957f8baafcefd4c9f72b7e3f3fafb7fcb3ca805dc69d242aef656e0736490
        Copying blob sha256:dbd31e1d863d4a41565c08ad1d419c3a3538abfdd4a7971de63b8c5c8a43caec
        Copying blob sha256:2f8531d5a6ece34772cf99a2d30e3057c636f1ad05cdec0c8009eab401e616a7
        Copying blob sha256:1dbcab28ce46b65c0174e5e82658492107396fead31e9144c343e6bc96e471c7
        Copying blob sha256:2e178fd72baf28bc587b5d274574f1a3d3e25ac802fdaf154af258a3c5891831
        Copying blob sha256:2912e793bf3d1505b5d6f84f00b3e1f7c93c9aca610730896f448a89e9736a3d
        Copying config sha256:99094e35636901d0eebf3e0bb9acfc83007a0748982d102232c661889dcd3ce3
        Writing manifest to image destination
        Storing signatures
        FATAL:   While making image from oci registry: while building SIF from layers: conveyor failed to get: no descriptor found for reference "ccee1f6ebb924fd0b3b6db646a51dabc905697aa25be132386dd490c2318286c"
    -[nf-core/rnaseq] 5/5 samples passed STAR 5% mapped threshold:
        6.62%: RAP1_UNINDUCED_R1
        6.77%: WT_R2
        6.38%: RAP1_UNINDUCED_R2
        7.08%: RAP1_IAA_30M_R1
        7.87%: WT_R1
    -
    -[nf-core/rnaseq] Pipeline completed with errors-
    WARN: Killing pending tasks (2)
    WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

Merci d'avance pour votre aide,

Guillaume

3

Bonjour,
sur un autre cluster je sais que la version 2.0 de nf-core/rnaseq posait pb pour les téléchargements d'images. L'utilisateur concerné par ce pb avait du télécharger les 6 images a la mano avant de pouvoir utiliser le pipeline.
Mais il y a déjà une version 3 de nf-core/rnaseq qui elle ne pose pas de pb d'image.
Voici les commandes :

singularity pull  --name quay.io-biocontainers-bioconductor-summarizedexperiment-1.18.1--r40_0.img.pulling.1605268292414 docker://quay.io/biocontainers/bioconductor-summarizedexperiment:1.18.1--r40_0 
singularity pull  --name quay.io-biocontainers-fastqc-0.11.9--0.img.pulling.1605799597310 docker://quay.io/biocontainers/fastqc:0.11.9--0
singularity pull  --name quay.io-biocontainers-bedtools-2.29.2--hc088bd4_0.img.pulling.1605799917165 docker://quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0 > /dev/null
singularity pull  --name quay.io-biocontainers-stringtie-2.1.4--h7e0af3c_0.img.pulling.1605800088310 docker://quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0
singularity pull  --name quay.io-biocontainers-rseqc-3.0.1--py37h516909a_1.img.pulling.1605800425876 docker://quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1
singularity pull  --name quay.io-biocontainers-qualimap-2.2.2d--1.img.pulling.1605800565837 docker://quay.io/biocontainers/qualimap:2.2.2d--1 > /dev/null
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4

Bonjour,
Merci beaucoup pour ces informations.
J'ai testé avec la version 3.0 et ça fonctionne bien !

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