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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm #741

Open winni-liu opened 4 years ago

winni-liu commented 4 years ago

Describe the issue

Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 290, <__ANONIO__> line 8364

System

Full VEP command line

vep --cache --dir_cache ../database/ --species canis_familiaris --force_overwrite --hgvs --refseq --cache_version 99 -i sample.vcf -o sample.vep

Full error message

Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationTy pe/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationTy pe/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationTy pe/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationTy pe/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationTy pe/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/AnnotationTy pe/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep/share/ensembl-vep-95.0-1/modules/Bio/EnsEMBL/VEP/Stats.pm lin e 365, <__ANONIO__> line 8364. 2020-04-23 09:10:41 - INFO: Database will be accessed when using --hgvs 2020-04-23 09:10:41 - INFO: Database will be accessed when using --hgvsc 2020-04-23 09:10:41 - INFO: Database will be accessed when using --hgvsp

dglemos commented 4 years ago

Hi, You're using vep version 95 and cache 99, you should use the same version for both. Can you also send your input file to try to replicate the issue?

winni-liu commented 4 years ago

hi, I change the vep version to 99: ensembl : 99.d3e7d31 ensembl-funcgen : 99.0832337 ensembl-io : 99.441b05b ensembl-variation : 99.642e1cd ensembl-vep : 99.2 and I use this command run it again, vep --cache --dir_cache ../database/ --species canis_familiaris --force_overwrite --hgvs --refseq --cache_version 99 -i sample.vcf -o sample.ncbi.vep &>log & I will get error message and the output file 'sample.ncbi.vep' is creat which have been annotationed, I just cannot understand this error message whether will affect my output. the new error message: Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 276, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm line 290, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. ... Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. Use of uninitialized value in hash element at /psd/biosoft/anaconda/envs/ensembl-vep_99/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Stats.pm line 365, <__ANONIO__> line 8364. 2020-04-26 10:18:37 - INFO: Database will be accessed when using --hgvs 2020-04-26 10:18:37 - INFO: Database will be accessed when using --hgvsc 2020-04-26 10:18:37 - INFO: Database will be accessed when using --hgvsp if I don't use the "--refseq", I will not get error message, so, error message just appear only I use the '--refseq'. also, the cache is succeeded creat,

2020-04-22 09:08:07 - Processing canis_familiaris 2020-04-22 09:08:07 - Processing version 95_CanFam3.1 2020-04-22 09:08:07 - No unprocessed types remaining, skipping 2020-04-22 09:08:07 - Processing felis_catus_refseq 2020-04-22 09:08:07 - Processing version 99_Felis_catus_9.0 2020-04-22 09:08:07 - Processing _var cache type ^M[> ] [ 0% ]^M[> ] [ 0% ]... 2020-04-22 09:12:14 - Processing felis_catus 2020-04-22 09:12:14 - Processing version 95_Felis_catus_9.0 2020-04-22 09:12:14 - No unprocessed types remaining, skipping 2020-04-22 09:12:14 - Processing tmp 2020-04-22 09:12:14 - Processing canis_familiaris_refseq 2020-04-22 09:12:14 - Processing version 99_CanFam3.1 2020-04-22 09:12:14 - Processing _var cache type ^M[> ] [ 0% ]^M[> ] [ 1% ].... 2020-04-22 09:18:16 - All done! I have attached my input vcf(sample.txt), for attach the file, 'sample.vcf' in the command line was moved 'sample.txt' sample.txt

dglemos commented 4 years ago

I can reproduce the issue. It looks like there's a problem with some of the RefSeq transcripts, some gene symbols are missing. That means that in your output, some variants are missing the gene, for example: 1 5070565 G/T We are looking into the issue and we'll let you know of any updates.

dglemos commented 4 days ago

Hi @winni-liu, We have added missing RefSeq gene symbols to the caches. Can you please run your command with the latest vep to make sure the data is not missing anymore?