snpeff : wont recognize the gtf or gff3 files (runtime exception)
Hi,
I am trying to build a custom databasee for snpeff.
As instructed both in the forum and snpeff instructions, I did the following;
Then I added the following into snpEff.config
file
# BG94_1
BG94_1.genome : BG94_1
Then I added a gff3 file (tried with gtf too) in to the path/to/snpeff-5.0.1/data/BG94_1
folder together with BG94_1.fa (both gzipped)
Then I ran the following command (please note that I am using bioconda installation of snpeff).
snpEff build -gff3 -v BG94_1
I am getting the following error;
0
0:00:00 SnpEff version SnpEff 5.0e (build 2021-03-09 06:01), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'BG94_1'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'BG94_1'
00:00:00 Reading config file: /Users/venura/miniconda3/pkgs/snpeff-5.0-hdfd78af_1/share/snpeff-5.0-1/data/BG94_1/snpEff.config
00:00:00 Reading config file: /Users/venura/miniconda3/envs/py38/share/snpeff-5.0-1/snpEff.config
00:00:00 done
Reading GFF3 data file : '/Users/venura/miniconda3/envs/py38/share/snpeff-5.0-1/./data/BG94_1/genes.gff'
java.lang.RuntimeException: File not found '/Users/venura/miniconda3/envs/py38/share/snpeff-5.0-1/./data/BG94_1/genes.gff'
at org.snpeff.util.Gpr.reader(Gpr.java:536)
at org.snpeff.util.Gpr.reader(Gpr.java:507)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readGff(SnpEffPredictorFactoryGff.java:488)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:341)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:370)
at org.snpeff.SnpEff.run(SnpEff.java:1188)
at org.snpeff.SnpEff.main(SnpEff.java:168)
java.lang.RuntimeException: Error reading file '/Users/venura/miniconda3/envs/py38/share/snpeff-5.0-1/./data/BG94_1/genes.gff'
java.lang.RuntimeException: File not found '/Users/venura/miniconda3/envs/py38/share/snpeff-5.0-1/./data/BG94_1/genes.gff'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:357)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:370)
at org.snpeff.SnpEff.run(SnpEff.java:1188)
at org.snpeff.SnpEff.main(SnpEff.java:168)
00:00:00 Logging
00:00:01 Checking for updates...
00:00:03 Done.
Here are some lines from my gff3 file;
#gff-version 3
Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 1 1345 . + . ID=gene_1;Name=Os01g0293800 gene;coverage=0.997;sequence_ID=0.982;extra_copy_number=0;copy_num_ID=gene_1_0
Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 1623 3128 . - . ID=gene_6;Name=Os01g0293900 gene;coverage=0.999;sequence_ID=0.968;extra_copy_number=0;copy_num_ID=gene_6_0
Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 20379 21605 . - . ID=gene_7;Name=Os01g0294500 gene;coverage=0.999;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_7_0
Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 48673 50214 . - . ID=gene_5;Name=Os01g0294700 gene;coverage=1.0;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_5_0
Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 102125 104501 . - . ID=gene_4;Name=Os01g0295600 gene;coverage=1.0;sequence_ID=0.992;extra_copy_number=0;copy_num_ID=gene_4_0
Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 105502 108051 . - . ID=gene_3;Name=Os01g0295700 gene;coverage=0.996;sequence_ID=0.991;extra_copy_number=0;copy_num_ID=gene_3_0
I am wondering why this is happening.
• 259 views
Finally, I made the custom database. Adding steps here just in case someone else needs it.
First, I added my database entries into the snpEff.config
file.
# BG94_1
BG94_1.genome : BG94_1
Since my genes.gff3
file continued to give troubles, I used @Juke34’s AGAT gff2gtf script and converted the file to .gtf
(version matters) using the following command.
agat_convert_sp_gff2gtf.pl -gff genes.gff3 --gtf_version 2.2 -o genes.gtf
Then I included the annotation file (genes.gtf
) together with sequence sequences.fa
file inside the predefined folder for the database (my case its /Users/venura/miniconda3/pkgs/snpeff-5.0-hdfd78af_1/share/snpeff-5.0-1/data/BG94_1
).
Then I used the following command (inside the snpeff-5.0-1
folder to build the database)
java -jar snpEff.jar build -gtf22 -v BG94_1
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