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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 in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. #97

Open NicMAlexandre opened 3 months ago

NicMAlexandre commented 3 months ago

Hello, My config contains the following lines:

GENETIC_CODE_TABLE=1
GENETIC_CODE_TABLENAME=Standard
MITO_GENETIC_CODE_TABLE=2
MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial
PARENT_DIR=/home/Nicolas/SIFT
ORG=genus_species
ORG_VERSION=Species_v1.0
DBSNP_VCF_FILE=/home/Nicolas/SIFT/dbSNP/annotated_variants.vcf.gz
#Running SIFT4G, this path works for the Dockerfile
SIFT4G_PATH=/home/software/sift4g/bin/sift4g
#PROTEIN_DB needs to be uncompressed
PROTEIN_DB=/home/Nicolas/SNPEff/uniprot_sprot.fasta

Ive also created the following subdirectories within SIFT

mkdir chr-src #contains sequences.fa.gz
mkdir dbSNP #contains annotated_variants.vcf.gz
mkdir gene-annotation-src #contains genes.gtf.gz and protein.pep.all.fa.gz

I run the following commands:

docker run -it --user $(id -u):$(id -g) -v /home/Nicolas/SIFT:/home/Nicolas/SIFT sift4g_db /bin/bash

perl make-SIFT-db-all.pl -config /home/Nicolas/SIFT/Species_SIFT.config.txt

Following some initialized responses, I get these messages:

Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.

My fasta folder remains empty along with my SIFT_prediction folder

DodotheMath commented 3 months ago

This mimics the output seen in issue:

https://github.com/pauline-ng/SIFT4G_Create_Genomic_DB/issues/95

But this previous issue was closed by the author.