No annotation results from plugins using Singularity

[yotsa]

I used singularity to run vep and it works fine, except that the annotation of plugins (in this case Blosum62 and NMD) didn't show up in the output vcf. I've tried to specify plugin directory but without success.

System

• VEP version: 112
• VEP Cache version: 112
• Perl version:
• OS: Ubuntu 22.04
• tabix installed ?

Full VEP command line

singularity exec -B /scratch/vep:/opt/vep/.vep \ -B /scratch/merge:/input \ /scratch/vep/vep112.sif \ vep --dir /opt/vep/.vep \ --cache --offline --format vcf --vcf --force_overwrite \ --fork 64 \ -i /opt/vep/.vep/G2.tmp.vcf \ -o /opt/vep/.vep/G2_vep.vcf \ --stats_file G2_stats.txt \ --everything \ --plugin Blosum62 \ --plugin NMD \ --verbose

Full error message

INFO: underlay of /etc/localtime required more than 50 (94) bind mounts 2024-05-23 00:42:23 - Ignored unsupported option 'no_update=1' from environment variable VEP_NO_UPDATE 2024-05-23 00:42:23 - Ignored unsupported option 'no_plugins=1' from environment variable VEP_NO_PLUGINS 2024-05-23 00:42:23 - Ignored unsupported option 'pluginsdir=/plugins' from environment variable VEP_PLUGINSDIR 2024-05-23 00:42:23 - Set 'dir_plugins=/plugins' from environment variable VEP_DIR_PLUGINS 2024-05-23 00:42:23 - Ignored unsupported option 'no_htslib=1' from environment variable VEP_NO_HTSLIB 2024-05-23 00:42:23 - Read configuration from environment variables 2024-05-23 00:42:23 - INFO: Disabling --hgvs; using --offline and no FASTA file found

[nuno-agostinho]

Hi @yotsa,

Thanks for your question. It could be that the input variants that you are using simply give no results for the NMD and Blosum62 plugins.

Please test VEP with these variants. You are supposed to get NMD and Blosum62 results for some of them:

1 11022 rs28775022 G A,T
1 7936271 . N N[12:58877476[,N[8:56445865[
1 2642609 . G A
1 119140608 rs139548132 A C,G,T
1 230710048 rs699 A G
4 89828156 rs201106962 A C
16 1314031 . A T
18  23873048  rs867018739  C  T
19 804947 rs569478349 G C
19  39735004  . A  C
19 39735057 rs752685201 G T
19 39737938 rs753930790 G A
19 45687010 rs1964272 G A
22 18610830 . T G

Best regards, Nuno

[yotsa]

Hi @nuno-agostinho

Thanks for the reply. I tested the variants you provided with blosum and nmd plugins, I only got blosum results but not nmd.

Do you have any other suggestions?

Yot

[nuno-agostinho]

Hi @yotsa,

Can you run VEP using the following variants with the NMD plugin? All of them should return NMD results:

8   1771100 370918  CT  C
8   1771101 287509  T   G
8   1771256 556933  GC  G   

Thanks, Nuno