I am having problems with the snpEff during the build running process

[hosseinidf]

Describe the issue I am analyzing whole genome sequencing(WGS) data in rice(Oryza.sativa) plants. When I use the following command to create the rice database, I encounter this problem. It should be noted that rice information is not available in the snpEFF.config file.

To Reproduce

1. SnpEff version:5.2c
2. Genome version:
3. SnpEff full command line: java -jar snpEff.jar build -gtf22 Rice
4. Output / Error message: . File '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/genes.gtf' line 113 'AP014957.1 DDBJ CDS 140150 141415 . + 0 transcript_id "gene-OSNPB_010102400"; gene_id "gene-OSNPB_010102400"; gene_name "Os01g0102400";' WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'gene-OSNPB_010102500'. Created transcript 'gene-OSNPB_010102500' and gene 'gene-OSNPB_010102500' for AP014957.1 DDBJ CDS 142083142630 + gene_id : gene-OSNPB_010102500 gene_name : Os01g0102500 transcript_id : gene-OSNPB_010102500 . File '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/genes.gtf' line 114 'AP014957.1 DDBJ CDS 142084 142631 . + 0 transcript_id "gene-OSNPB_010102500"; gene_id "gene-OSNPB_010102500"; gene_name "Os01g0102500";' WARNING_TRANSCRIPT_NOT_FOUND: Too many 'WARNING_TRANSCRIPT_NOT_FOUND' warnings, no further warnings will be shown. WARNING_CANNOT_ADD_UTR: Could not add UTR. File '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/genes.gtf' line 14796 'AP014957.1 DDBJ five_prime_UTR 26249386 26249406 . + . transcript_id "gene-OSNPB_010650200"; gene_id "gene-OSNPB_010650200"; gene_name "Os01g0650200";' WARNING_CANNOT_ADD_UTR: Could not add UTR. File '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/genes.gtf' line 27405 'AP014957.1 DDBJ five_prime_UTR 41251235 41251326 . + . transcript_id "gene-OSNPB_010939700"; gene_id "gene-OSNPB_010939700"; gene_name "Os01g0939700";' WARNING_CANNOT_ADD_UTR: Could not add UTR. File '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/genes.gtf' line 27424 'AP014957.1 DDBJ three_prime_UTR 41271897 41272093 . + . transcript_id "gene-OSNPB_010939700-3"; gene_id "gene-OSNPB_010939700-3"; gene_name "Os01g0939700";' ERROR: CDS check file '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/cds.fa' not found. ERROR: Protein check file '/home/foad/NGS-Book/Chapter3-WGS/Reference_based_analysis/data/Rice/protein.fa' not found. ERROR: Database check failed.

Data genes.gtf: AP014957.1 DDBJ CDS 3449 3616 . + 0 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 4357 4455 . + 0 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 5457 5560 . + 0 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 7136 7944 . + 1 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 8028 8150 . + 2 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 8232 8320 . + 2 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 8408 8608 . + 0 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 9210 9615 . + 0 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 10102 10187 . + 2 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100"; AP014957.1 DDBJ CDS 10274 10297 . + 0 transcript_id "gene-OSNPB_010100100"; gene_id "gene-OSNPB_010100100"; gene_name "Os01g0100100";

sequences.fa:

AP014957.1 Oryza sativa Japonica Group DNA, chromosome 1, cultivar: Nipponbare, complete sequence NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC

snp.configs: The last lines of this file

Ebola virus

ebola_zaire.genome: Ebola Zaire Virus KJ660346.1

Ursidibacter maritimus

lekn01.genome: Ursidibacter maritimus lekn01.reference: https://www.ncbi.nlm.nih.gov/Traces/wgs/LEKN01

Rice

Rice.genome : Rice

[MdUmar-tech]

Hi if u provide NCBI accession id , I will help u out , I have solved this problem