can't open files

[dodudoduding]

I have already installed swith.pm,and put all the files in the right place,can anyone help?Thanks.

converting gene format to use-able input Can't locate Switch.pm in @INC (you may need to install the Switch module) (@INC contains: /home/jiayi/miniconda3/lib/perl5/5.32/site_perl /home/jiayi/miniconda3/lib/perl5/site_perl /home/jiayi/miniconda3/lib/perl5/5.32/vendor_perl /home/jiayi/miniconda3/lib/perl5/vendor_perl /home/jiayi/miniconda3/lib/perl5/5.32/core_perl /home/jiayi/miniconda3/lib/perl5/core_perl .) at gff_gene_format_to_ucsc.pl line 4. BEGIN failed--compilation aborted at gff_gene_format_to_ucsc.pl line 4. done converting gene format making single records file can't open /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/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 /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/gene-annotation-src/noncoding.txt at make-single-records-noncoding.pl line 59. done making noncoding records make the fasta sequences can't open /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/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: '/media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/fasta/*.fasta': No such file or directory /media/data2/jiayi/sift4g/bin/sift4g -d /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/gene-annotation-src/Kandelia_rename20210915.pro.fasta -q /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/all_prot.fasta --subst /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/subst --out /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/SIFT_predictions --sub-results Checking query data and substitutions files

EXITING! No valid queries to process.

[pauline-ng]

Where do you have Switch installed and how did you install it?

Thanks, Pauline

[dodudoduding]

Where do you have Switch installed and how did you install it?

Thanks, Pauline

/usr/share/perl5/Switch.pm.I install it by sudo apt-get install libswitch-perl. And was the file error caused by the switch?Thanks

[pauline-ng]

Try typing this in the terminal and then running SIFT in the same terminal

export PERLLIB="$PERLLIB:/usr/share/perl5"
export PERL5LIB="$PERL5LIB:/usr/share/perl5"

If it works, add the environmental variable to your .bashrc

[dodudoduding]

Thanks so much,this problem is solved.But it still can't recognize my file like this: converting gene format to use-able input Unable to open for reading done converting gene format making single records file can't open /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/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 /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/gene-annotation-src/noncoding.txt at make-single-records-noncoding.pl line 59. done making noncoding records make the fasta sequences can't open /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/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: '/media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/fasta/*.fasta': No such file or directory /media/data2/jiayi/sift4g/bin/sift4g -d /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/gene-annotation-src/Kandelia_rename20210915.pro.fasta -q /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/all_prot.fasta --subst /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/subst --out /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/SIFT_predictions --sub-results Checking query data and substitutions files

EXITING! No valid queries to process.

[pauline-ng]

Does it work on the test file? If it works on the test examples, check that your gff (gene file) is in the correct format.

[dodudoduding]

Does it work on the test file? If it works on the test examples, check that your gff (gene file) is in the correct format.

The test files can work,are the problems exerted by the wrong format?Are there other probabilities cause the problems such as wrong path?

[pauline-ng]

Check you have read/write permission for your folders and gff file.

[dodudoduding]

Check you have read/write permission for your folders and gff file. Yes I do have.Let me check the format again,thanks.

[dodudoduding]

Check you have read/write permission for your folders and gff file.

Besides,I have another question,which file has a wrong format?Only the protein or all of them?Thanks.

converting gene_ format to use-able input Unable to open for reading done converting gene format making single records file can't open /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/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 /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/gene-annotation-src/noncoding.txt at make-single-records-noncoding.pl line 59. done making noncoding records make the fasta sequences can't open /media/data2/jiayi/sift4g/scripts_to_build_SIFT_db/test_files/kandelia_obovata/gene-annotation-src/protein_coding_genes.txt at generate-fasta-subst-files-BIOPERL.pl line 387. done making the fasta sequences

[pauline-ng]

Probably just the gene file. Check that it's similar in format to the examples.