Hi all,
just run coovar on sars-cov2 vcf - all annotations were downloaded from ensemble, but I keep having this error regarding the cds regions, any advice? I did use --feature_source --feature_type but no difference...
ibseq@C02DW5NDMD6T Desktop % perl coovar-0.07/coovar.pl -e ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 -r ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa -v ../Downloads/test_barcode10.merged.vcf -o OUTPUT_DIRECTORY_10 --circos --feature_source --feature_type 'CDS'
[coovar.pl] Start executing script on Fri Jan 22 12:55:04 2021
[coovar.pl] Operating system: darwin darwin-thread-multi-2level
[coovar.pl] Program directory: coovar-0.07
[coovar.pl] Program version: 0.07
[coovar.pl] Command line: coovar-0.07/coovar.pl -e ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 -r ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa -v ../Downloads/test_barcode10.merged.vcf -o OUTPUT_DIRECTORY_10 --circos --feature_source --feature_type CDS
[coovar.pl] REFERENCE: ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa
[coovar.pl] CODING EXONS: ../Downloads/Sars_cov_2.ASM985889v3.101.gff3
[coovar.pl] GVS_TAB_FORMAT:
[coovar.pl] GVS_VCF_FORMAT: ../Downloads/test_barcode10.merged.vcf
[coovar.pl] OUTPUT DIRECTORY: OUTPUT_DIRECTORY_10
[coovar.pl] CIRCOS FLAG: 1
[coovar.pl] FEATURE SOURCE: --feature_type
[coovar.pl] FEATURE TYPE: CDS
[coovar.pl] Indexing FASTA file ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa on Fri Jan 22 12:55:04 2021
[coovar.pl] Done indexing FASTA file on Fri Jan 22 12:55:04 2021
[coovar.pl] Extracting contig information from FASTA on Fri Jan 22 12:55:04 2021
[coovar.pl] Parsing GV files on Fri Jan 22 12:55:04 2021
[vcf2cv.pl] Start executing script on Fri Jan 22 12:55:04 2021
[vcf2cv.pl] Parsing VCF input file on Fri Jan 22 12:55:04 2021
[vcf2cv.pl] 1 SNPs written to OUTPUT_DIRECTORY_10/intermediate-files/test_barcode10.merged.vcf.snp...
[vcf2cv.pl] 0 insertions written to OUTPUT_DIRECTORY_10/intermediate-files/test_barcode10.merged.vcf.ins...
[vcf2cv.pl] 0 deletions written to OUTPUT_DIRECTORY_10/intermediate-files/test_barcode10.merged.vcf.del...
[vcf2cv.pl] Done at Fri Jan 22 12:55:04 2021
[coovar.pl] Checking consistency of GV files on Fri Jan 22 12:55:04 2021
[revise-gv-files.pl] Start executing script on Fri Jan 22 12:55:04 2021
[revise-gv-files.pl] Reading contig information from OUTPUT_DIRECTORY_10/intermediate-files/contigs.summary on Fri Jan 22 12:55:04 2021
[revise-gv-files.pl] Revising SNPs... on Fri Jan 22 12:55:04 2021
[revise-gv-files.pl] 1 kept SNPs written to OUTPUT_DIRECTORY_10/snps/kept_test_barcode10.merged.vcf.snp
[revise-gv-files.pl] Revising insertions... on Fri Jan 22 12:55:04 2021
[revise-gv-files.pl] 0 kept insertions written to OUTPUT_DIRECTORY_10/insertions/kept_test_barcode10.merged.vcf.ins
[revise-gv-files.pl] Revising deletions... on Fri Jan 22 12:55:04 2021
[revise-gv-files.pl] 0 kept deletions written to OUTPUT_DIRECTORY_10/deletions/kept_test_barcode10.merged.vcf.del
[revise-gv-files.pl] Done at Fri Jan 22 12:55:04 2021
[coovar.pl] Extracting cDNA sequence from reference on Fri Jan 22 12:55:04 2021
[extract-cdna.pl] Start executing script on Fri Jan 22 12:55:04 2021
[extract-cdna.pl] Filtering and sorting input GFF/GTF file ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 ...
[extract-cdna.pl] ERROR: Could not find coding sequence (CDS) entries in file ../Downloads/Sars_cov_2.ASM985889v3.101.gff3. Please make sure that this files contains features of type 'CDS' and of source '--feature_type' (see README).
[coovar.pl] ERROR executing command: perl coovar-0.07/scripts/extract-cdna.pl ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa OUTPUT_DIRECTORY_10 CDS --feature_type
. at coovar-0.07/coovar.pl line 42.
Hi all, just run coovar on sars-cov2 vcf - all annotations were downloaded from ensemble, but I keep having this error regarding the cds regions, any advice? I did use --feature_source --feature_type but no difference...
ibseq@C02DW5NDMD6T Desktop % perl coovar-0.07/coovar.pl -e ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 -r ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa -v ../Downloads/test_barcode10.merged.vcf -o OUTPUT_DIRECTORY_10 --circos --feature_source --feature_type 'CDS' [coovar.pl] Start executing script on Fri Jan 22 12:55:04 2021 [coovar.pl] Operating system: darwin darwin-thread-multi-2level [coovar.pl] Program directory: coovar-0.07 [coovar.pl] Program version: 0.07 [coovar.pl] Command line: coovar-0.07/coovar.pl -e ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 -r ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa -v ../Downloads/test_barcode10.merged.vcf -o OUTPUT_DIRECTORY_10 --circos --feature_source --feature_type CDS [coovar.pl] REFERENCE: ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa [coovar.pl] CODING EXONS: ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 [coovar.pl] GVS_TAB_FORMAT: [coovar.pl] GVS_VCF_FORMAT: ../Downloads/test_barcode10.merged.vcf [coovar.pl] OUTPUT DIRECTORY: OUTPUT_DIRECTORY_10 [coovar.pl] CIRCOS FLAG: 1 [coovar.pl] FEATURE SOURCE: --feature_type [coovar.pl] FEATURE TYPE: CDS [coovar.pl] Indexing FASTA file ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa on Fri Jan 22 12:55:04 2021 [coovar.pl] Done indexing FASTA file on Fri Jan 22 12:55:04 2021 [coovar.pl] Extracting contig information from FASTA on Fri Jan 22 12:55:04 2021 [coovar.pl] Parsing GV files on Fri Jan 22 12:55:04 2021 [vcf2cv.pl] Start executing script on Fri Jan 22 12:55:04 2021 [vcf2cv.pl] Parsing VCF input file on Fri Jan 22 12:55:04 2021 [vcf2cv.pl] 1 SNPs written to OUTPUT_DIRECTORY_10/intermediate-files/test_barcode10.merged.vcf.snp... [vcf2cv.pl] 0 insertions written to OUTPUT_DIRECTORY_10/intermediate-files/test_barcode10.merged.vcf.ins... [vcf2cv.pl] 0 deletions written to OUTPUT_DIRECTORY_10/intermediate-files/test_barcode10.merged.vcf.del... [vcf2cv.pl] Done at Fri Jan 22 12:55:04 2021 [coovar.pl] Checking consistency of GV files on Fri Jan 22 12:55:04 2021 [revise-gv-files.pl] Start executing script on Fri Jan 22 12:55:04 2021 [revise-gv-files.pl] Reading contig information from OUTPUT_DIRECTORY_10/intermediate-files/contigs.summary on Fri Jan 22 12:55:04 2021 [revise-gv-files.pl] Revising SNPs... on Fri Jan 22 12:55:04 2021 [revise-gv-files.pl] 1 kept SNPs written to OUTPUT_DIRECTORY_10/snps/kept_test_barcode10.merged.vcf.snp [revise-gv-files.pl] Revising insertions... on Fri Jan 22 12:55:04 2021 [revise-gv-files.pl] 0 kept insertions written to OUTPUT_DIRECTORY_10/insertions/kept_test_barcode10.merged.vcf.ins [revise-gv-files.pl] Revising deletions... on Fri Jan 22 12:55:04 2021 [revise-gv-files.pl] 0 kept deletions written to OUTPUT_DIRECTORY_10/deletions/kept_test_barcode10.merged.vcf.del [revise-gv-files.pl] Done at Fri Jan 22 12:55:04 2021 [coovar.pl] Extracting cDNA sequence from reference on Fri Jan 22 12:55:04 2021 [extract-cdna.pl] Start executing script on Fri Jan 22 12:55:04 2021 [extract-cdna.pl] Filtering and sorting input GFF/GTF file ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 ... [extract-cdna.pl] ERROR: Could not find coding sequence (CDS) entries in file ../Downloads/Sars_cov_2.ASM985889v3.101.gff3. Please make sure that this files contains features of type 'CDS' and of source '--feature_type' (see README). [coovar.pl] ERROR executing command: perl coovar-0.07/scripts/extract-cdna.pl ../Downloads/Sars_cov_2.ASM985889v3.101.gff3 ../Downloads/Sars_cov_2.ASM985889v3.dna.toplevel.fa OUTPUT_DIRECTORY_10 CDS --feature_type . at coovar-0.07/coovar.pl line 42.