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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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snpEff GRCm38 singularity image error #461

Closed mncfletcher closed 2 years ago

mncfletcher commented 2 years ago

Hello sarek maintainers,

I'm trying to run snpEff (sarek v2.7.1, Nextflow v21.04.3) on mouse WGS data aligned to the GRCm38 reference. I saw in another issue reported here that snpEff this reference genome should be supported, but I got the following error - what's the best way to solve this?

Thanks very much!

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'Snpeff (BKO_tumour - Strelka - Strelka_BKO_tumour_variants.vcf.gz)'

Caused by: Failed to pull singularity image command: singularity pull --name nfcore-sareksnpeff-2.7.1.GRCm38.img.pulling.1638179895467 docker://nfcore/sareksnpeff:2.7.1.GRCm38 > /dev/null status : 143 message: [34mINFO:  Converting OCI blobs to SIF format INFO:  Starting build... Getting image source signatures Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3 Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b Copying blob sha256:3fbba84366ddeb8b6dece9fb1c547db6afa6e727c4bfe599a5ca2cfdff4c964e Copying blob sha256:dab4755957b222abf14671238b44d656dda9912c5cfce0181b0f0f6752e6cc7f Copying blob sha256:65f4224a243e8f0db3777f98e62dd2a01d18fb0f2db90188b0c7a04fd49967ec Copying blob sha256:3a96f9b571ed978d10eff21993389ffa94fc0931fa91654573e08f26a45921b5 Copying blob sha256:b427d20953ff85692680e09f7cd56bb2c485243e615146f7700b0446a672b6b9 Copying config sha256:124da0780772bc69760ba31827ce13ca0fee9bd6b6cd2f945871c613e372aa0f Writing manifest to image destination Storing signatures 2021/11/29 11:00:04 info unpack layer: sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b 2021/11/29 11:00:08 warn xattr{etc/gshadow} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2021/11/29 11:00:08 warn xattr{/omics/groups/OE0014/internal/BCAT1_TME_Pavle/analysis/nf-sarek/work/rootfs-e0c384a7-50fa-11ec-a8db-e41f13814edf/etc/gshadow} destination filesystem does not support xattrs, further warnings will be suppressed 2021/11/29 11:01:52 info unpack layer: sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3 2021/11/29 11:01:54 warn xattr{etc/gshadow} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2021/11/29 11:01:54 warn xattr{/omics/groups/OE0014/internal/BCAT1_TME_Pavle/analysis/nf-sarek/work/rootfs-e0c384a7-50fa-11ec-a8db-e41f13814edf/etc/gshadow} destination filesystem does not support xattrs, further warnings will be suppressed 2021/11/29 11:06:16 info unpack layer: sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b 2021/11/29 11:09:18 info unpack layer: sha256:3fbba84366ddeb8b6dece9fb1c547db6afa6e727c4bfe599a5ca2cfdff4c964e 2021/11/29 11:09:20 warn xattr{var/cache/apt/archives/partial} ignoring ENOTSUP on setxattr "user.rootlesscontainers" 2021/11/29 11:09:20 warn xattr{/omics/groups/OE0014/internal/BCAT1_TME_Pavle/analysis/nf-sarek/work/rootfs-e0c384a7-50fa-11ec-a8db-e41f13814edf/var/cache/apt/archives/partial} destination filesystem does not support xattrs, further warnings will be suppressed 2021/11/29 11:09:21 info unpack layer: sha256:dab4755957b222abf14671238b44d656dda9912c5cfce0181b0f0f6752e6cc7f 2021/11/29 11:09:21 info unpack layer: sha256:65f4224a243e8f0db3777f98e62dd2a01d18fb0f2db90188b0c7a04fd49967ec 2021/11/29 11:16:50 info unpack layer: sha256:3a96f9b571ed978d10eff21993389ffa94fc0931fa91654573e08f26a45921b5 2021/11/29 11:17:08 info unpack layer: sha256:b427d20953ff85692680e09f7cd56bb2c485243e615146f7700b0446a672b6b9 INFO:  Creating SIF file...

maxulysse commented 2 years ago

Hi @mncfletcher The docker container does exist: https://hub.docker.com/r/nfcore/sareksnpeff So I assume your problem is due to Singularity not being able to download and convert the container from Dockerhub within the Nextflow process. I'd recommend trying to download the Singularity image separately, with the singularity pull --name nfcore-sareksnpeff-2.7.1.GRCm38.img docker://nfcore/sareksnpeff:2.7.1.GRCm38 command. If you're using the NXF_SINGULARITY_CACHEDIR or similar env variables or options in Nextlfow, please do so in the right path. Otherwise I'd recommend to use that. By default, it should be in the work/singularity folder.