Plugin 'dbNSFP' of VEP went wrong
Entering edit mode
4.6 years ago
RC • 0

Hi there, We met a syntax error when we using VEP with to annotate variants.

perl /home/zoeching/Tools/src/ensembl-tools/scripts/variant_effect_predictor/\
--offline \
--fork 10\
--merged /home/zoeching/pku/Ref\
 --everything \
--vcf \
--vcf_info_field CSQ\
--plugin dbNSFP,/home/zoeching/pku/Ref/dbNSFPv2.9.1/dbNSFP.gz,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,CADD_raw,CADD_raw_rankscore,CADD_phred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore\
--plugin LoF,human_ancestor_fa:/home/zoeching/pku/Ref/human_ancestor.fa.gz\
-i /work1/ASD/Data/other/ASD569_1.gatk-queue_raw_snps.vcf \
-o  ASD569_1.gatk-queue_raw_ann_snps.vcf

after ran the command, I got this:

The output (if any) follows:

2016-09-04 16:02:10 - Read existing cache info 2016-09-04 16:02:10 - INFO: Disabling --hgvs; using --offline and no FASTA file found 2016-09-04 16:02:10 - Failed to compile plugin dbNSFP: syntax error at /home/zoeching/Tools/library/perl_module/lib/perl5/ line 304, near "s/[|]/&/gr" Compilation failed in require at (eval 68) line 2. BEGIN failed--compilation aborted at (eval 68) line 2.

2016-09-04 16:02:11 - Loaded plugin: LoF 2016-09-04 16:02:11 - Starting... 2016-09-04 16:02:11 - Detected format of input file as vcf 2016-09-04 16:02:11 - Read 5000 variants into buffer 2016-09-04 16:02:11 - Calculating consequences

and this

Bareword found where operator expected at /home/zoeching/Tools/library/perl_module/lib/perl5/ line 304, near "s/[|]/&/gr" i didn't get the mean of "r" in "s/[|]/&/gr",line304

so i deleted "r" and ran the command again. At this time, no errors came out but the annotation failed. The columns for annotation from dbNSFP.gz were empty. And i can successfully use "chr pos" to grep infomation from dbNSFP2.9.1_variant.chr* file. So, the input file is okay.

Anyone met this error before? Anything wrong with 304)? What does the "r" means here?

annotate dbNSFP VEP software error • 2.4k views
Entering edit mode
4.6 years ago
EnsemblWill ▴ 560

Resolved on GitHub, please don't cross-post across help forums if you can avoid it!

Entering edit mode

OK. Thx for your help.


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