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pauline-ng / SIFT4G_Create_Genomic_DB

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.
GNU General Public License v3.0
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Cannot create own database #40

Closed zhansia closed 2 years ago

zhansia commented 3 years ago

Hi, pauline ng, I managed to create the example database, but when it come to create my own database, it pop out this error as show in below, can u help me to check...

entered mkdir ./test_files/coronavirus/ASM985889v3 converting gene format to use-able input Unable to open for reading done converting gene format making single records file can't open ./test_files/coronavirus/gene-annotation-src/protein_coding_genes.txt at make-single-records-BIOPERL.pl line 143. done making single records template making noncoding records file can't open ./test_files/coronavirus/gene-annotation-src/noncoding.txt at make-single-records-noncoding.pl line 59. done making noncoding records make the fasta sequences can't open ./test_files/coronavirus/gene-annotation-src/protein_coding_genes.txt at generate-fasta-subst-files-BIOPERL.pl line 387. done making the fasta sequences start siftsharp, getting the alignments cat: './test_files/coronavirus/fasta/*.fasta': No such file or directory /home/FYPuser/zhan/SIFT4G_Create_Genomic_DB-master/sift4g/bin/sift4g -d /home/FYPuser/zhan/SIFT4G_Create_Genomic_DB-master/uniref90.fasta -q ./test_files/coronavirus/all_prot.fasta --subst ./test_files/coronavirus/subst --out ./test_files/coronavirus/SIFT_predictions --sub-results Checking query data and substitutions files

EXITING! No valid queries to process.

pauline-ng commented 3 years ago

First 3 lines gives the error


converting gene format to use-able input
Unable to open for reading

it can't read your gene file.

zhansia commented 3 years ago

But I d put the Fasta file in gz format..I have tried multiple time still cannot

On Tue, 22 Dec 2020, 8:54 pm pauline-ng, notifications@github.com wrote:

First 3 lines gives the error

converting gene format to use-able input Unable to open for reading

it can't read your gene file.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pauline-ng/SIFT4G_Create_Genomic_DB/issues/40#issuecomment-749526071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQWGWQ2P2LGPHKGP7NXRUGLSWCJIVANCNFSM4VFQDVKQ .

pauline-ng commented 3 years ago

This error indicates SIFT can't read your gene file. It can read your fasta file.