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pauline-ng / SIFT4G_Create_Genomic_DB

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
GNU General Public License v3.0
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Use of uninitialized value $fasta_subseq in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 446, <IN_TX> line 37345. #59

Closed lizhiminlhy closed 2 years ago

lizhiminlhy commented 2 years ago

@pauline-ng Hi Pauline，

A big log file with repetitive warnings like "Use of uninitialized value $fasta_subseq in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 446, line 37345."

When I run the sample files, SIFT4G databases created correctly.

I look in the fasta directory for my file , I see protein sequences.

This is my file tree: |-- chr-src genomic.fa.gz |-- gene-annotation-src genomic.gtf.gz |-- dbSNP xx.vcf.gz

My config-file: GENETIC_CODE_TABLE=1 GENETIC_CODE_TABLENAME=Standard MITO_GENETIC_CODE_TABLE=5 MITO_GENETIC_CODE_TABLENAME=Invertebrate Mitochondrial

PARENT_DIR=/public/home/lizhimin/biosoft/sift4g/scripts_to_build_SIFT_db/hefeishi_test/hefeishi ORG=hefeishi ORG_VERSION=GRCh38.83

DBSNP_VCF_FILE=hefeishi.LDfilter-SRR-remove.vcf.gz

Running SIFT 4G

SIFT4G_PATH=~/anaconda3/bin/sift4g PROTEIN_DB=/public/home/lizhimin/biosoft/sift4g/scripts_to_build_SIFT_db/hefeishi_test/protein.faa

Any advice?

Thanks, LiZhimin

pauline-ng commented 2 years ago

Hi Liz,

You can just ignore that warning. I ignore it myself. :)

Best, Pauline