However, when I annotate the vcf file with java -Xmx10g -jar snpEff.jar -v NC_013638.1 -c snpEff.config -i vcf AA1_bwa.filt.vcf > AA1.vari.vcf, I got Errors:
OR
The log lines are:
00:00:00 SnpEff version SnpEff 5.0 (build 2020-10-04 16:02), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NC_013638.1'
00:00:00 Reading config file: /data/home/chuxl/software/snpEff/snpEff.config
00:00:02 done
00:00:02 Reading database for genome version 'NC_013638.1' from file '/data/home/chuxl/software/snpEff/./data/NC_013638.1/snpEffectPredictor.bin' (this might take a while)
00:00:02 done
00:00:02 Loading Motifs and PWMs
00:00:02 Building interval forest
00:00:02 done.
00:00:02 Genome stats :
-----------------------------------------------
Genome name : 'phagephi2'
Genome version : 'NC_013638.1'
Genome ID : 'NC_013638.1[0]'
Has protein coding info : true
Has Tr. Support Level info : true
Genes : 43
Protein coding genes : 43
-----------------------------------------------
Transcripts : 43
Avg. transcripts per gene : 1.00
TSL transcripts : 0
-----------------------------------------------
Checked transcripts :
AA sequences : 43 ( 100.00% )
DNA sequences : 0 ( 0.00% )
-----------------------------------------------
Protein coding transcripts : 43
Length errors : 0 ( 0.00% )
STOP codons in CDS errors : 0 ( 0.00% )
START codon errors : 0 ( 0.00% )
STOP codon warnings : 0 ( 0.00% )
UTR sequences : 0 ( 0.00% )
Total Errors : 0 ( 0.00% )
WARNING : No protein coding transcript has UTR
-----------------------------------------------
Cds : 43
Exons : 43
Exons with sequence : 43
Exons without sequence : 0
Avg. exons per transcript : 1.00
WARNING : No mitochondrion chromosome found
-----------------------------------------------
Number of chromosomes : 2
Chromosomes : Format 'chromo_name size codon_table'
So basically, nothing was annotated here. All the information about the reference sequence I have is from ncbi link. How can I get the annotation details of variations?
Hi,
I would like to use snpEff to annotate the variations in to synonymous non-synonymous mutations and to see the animo acid change caused by the mutations. I built the Pseudomonas phage phi-2 (https://www.ncbi.nlm.nih.gov/nuccore/281306659/) following the online instructions: https://pcingola.github.io/SnpEff/se_buildingdb/#option-4-building-a-database-from-genbank-files.
The .gbk file was download from ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/pseudomonas_phage_phi_2_uid42717 and put it in the snpEff/data/NC_013638.1/genes.gbk
The following information was added to snpEff.config file![image](https://user-images.githubusercontent.com/73734129/97827320-e38ef580-1cfe-11eb-8702-a00c3ae92d7b.png)
Then, I created database with the following line:
java -jar snpEff.jar build -genbank -v NC_013638.1
A .bin file was created: snpEff/data/NC_013638.1/snpEffectPredictor.bin with the following information
java -jar snpEff.jar build -genbank -v NC_013638.1 00:00:00 SnpEff version SnpEff 5.0 (build 2020-10-04 16:02), by Pablo Cingolani 00:00:00 Command: 'build' 00:00:00 Building database for 'NC_013638.1' 00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NC_013638.1' 00:00:00 Reading config file: /data/home/chuxl/software/snpEff/snpEff.config 00:00:02 done Chromosome: 'NC_013638.1 GI:281306659' length: 43144
00:00:02 Caracterizing exons by splicing (stage 1) :
00:00:02 Caracterizing exons by splicing (stage 2) : 00:00:02 done. 00:00:02 [Optional] Rare amino acid annotations 00:00:02 Warning: Cannot read optional protein sequence file '/data/home/chuxl/software/snpEff/./data/NC_013638.1/protein.fa', nothing done. 00:00:02 Protein check file: '/data/home/chuxl/software/snpEff/./data/NC_013638.1/genes.gbk'
00:00:02 Checking database using protein sequences 00:00:02 Comparing Proteins... Labels: '+' : OK '.' : Missing '*' : Error +++++++++++++++++++++++++++++++++++++++++++
00:00:02 Saving database 00:00:03 [Optional] Reading regulation elements: GFF 00:00:03 Warning: Cannot read optional regulation file '/data/home/chuxl/software/snpEff/./data/NC_013638.1/regulation.gff', nothing done. 00:00:03 [Optional] Reading regulation elements: BED 00:00:03 Cannot find optional regulation dir '/data/home/chuxl/software/snpEff/./data/NC_013638.1/regulation.bed/', nothing done. 00:00:03 [Optional] Reading motifs: GFF 00:00:03 Warning: Cannot open PWMs file /data/home/chuxl/software/snpEff/./data/NC_013638.1/pwms.bin. Nothing done 00:00:03 Done 00:00:03 Logging 00:00:04 Checking for updates... 00:00:07 Done.
However, when I annotate the vcf file with
OR
![image](https://user-images.githubusercontent.com/73734129/97827835-61073580-1d00-11eb-89ca-fd3aa142379d.png)
java -Xmx10g -jar snpEff.jar -v NC_013638.1 -c snpEff.config -i vcf AA1_bwa.filt.vcf > AA1.vari.vcf
, I got Errors:The log lines are:
00:00:00 SnpEff version SnpEff 5.0 (build 2020-10-04 16:02), by Pablo Cingolani 00:00:00 Command: 'ann' 00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NC_013638.1' 00:00:00 Reading config file: /data/home/chuxl/software/snpEff/snpEff.config 00:00:02 done 00:00:02 Reading database for genome version 'NC_013638.1' from file '/data/home/chuxl/software/snpEff/./data/NC_013638.1/snpEffectPredictor.bin' (this might take a while) 00:00:02 done 00:00:02 Loading Motifs and PWMs 00:00:02 Building interval forest 00:00:02 done. 00:00:02 Genome stats :
-----------------------------------------------
Genome name : 'phagephi2'
Genome version : 'NC_013638.1'
Genome ID : 'NC_013638.1[0]'
Has protein coding info : true
Has Tr. Support Level info : true
Genes : 43
Protein coding genes : 43
-----------------------------------------------
Transcripts : 43
Avg. transcripts per gene : 1.00
TSL transcripts : 0
-----------------------------------------------
Checked transcripts :
AA sequences : 43 ( 100.00% )
DNA sequences : 0 ( 0.00% )
-----------------------------------------------
Protein coding transcripts : 43
Length errors : 0 ( 0.00% )
STOP codons in CDS errors : 0 ( 0.00% )
START codon errors : 0 ( 0.00% )
STOP codon warnings : 0 ( 0.00% )
UTR sequences : 0 ( 0.00% )
Total Errors : 0 ( 0.00% )
WARNING : No protein coding transcript has UTR
-----------------------------------------------
Cds : 43
Exons : 43
Exons with sequence : 43
Exons without sequence : 0
Avg. exons per transcript : 1.00
WARNING : No mitochondrion chromosome found
-----------------------------------------------
Number of chromosomes : 2
Chromosomes : Format 'chromo_name size codon_table'
'NC_013638.1 GI:281306659' 43144 Bacterial_and_Plant_Plastid
'NC_013638.1' 1 Bacterial_and_Plant_Plastid
-----------------------------------------------
00:00:02 Predicting variants
ERRORS: Some errors were detected Error type Number of errors ERROR_CHROMOSOME_NOT_FOUND 5
00:00:02 Creating summary file: snpEff_summary.html 00:00:03 Creating genes file: snpEff_genes.txt 00:00:03 done. 00:00:03 Logging 00:00:04 Checking for updates... 00:00:07 Done.
So basically, nothing was annotated here. All the information about the reference sequence I have is from ncbi link. How can I get the annotation details of variations?
Thanks, Xiaolin