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.
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processing database part 975 than finish,and nothing generate #58
Hi,pauline-ng,it always processing database part 975,than done, it can not go next,so what happened ?i want know,it is a big problem that i can not resolve.
converting gene format to use-able input
done converting gene format
making single records file
done making single records template
making noncoding records file
done making noncoding records
make the fasta sequences
done making the fasta sequences
start siftsharp, getting the alignments
/home/Wangpengfei/anaconda3/envs/sift4g/bin/sift4g -d /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/nr -q /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/test_files/bovine_ncbi/all_prot.fasta --subst /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/test_files/bovine_ncbi/subst --out /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB
Checking query data and substitutions files
Hi,pauline-ng,it always processing database part 975,than done, it can not go next,so what happened ?i want know,it is a big problem that i can not resolve.
converting gene format to use-able input done converting gene format making single records file done making single records template making noncoding records file done making noncoding records make the fasta sequences done making the fasta sequences start siftsharp, getting the alignments /home/Wangpengfei/anaconda3/envs/sift4g/bin/sift4g -d /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/nr -q /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/test_files/bovine_ncbi/all_prot.fasta --subst /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB-master/test_files/bovine_ncbi/subst --out /home/Wangpengfei/sift4g/SIFT4G_Create_Genomic_DB Checking query data and substitutions files