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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Possible precedence issue with control flow operator at #95
@pauline-ng Hi, i would like to ask which file of my error is wrong?Looking forward to your reply.
this is my prossess:
perl make-SIFT-db-all.pl -config test_files/AK58V4MP.txt
converting gene format to use-able input
done converting gene format
making single records file
Possible precedence issue with control flow operator at /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm line 791.
Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274.
Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280.
Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274.
Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280.
Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274.
Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280.
Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274.
Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.
@pauline-ng Hi, i would like to ask which file of my error is wrong?Looking forward to your reply.
this is my prossess: perl make-SIFT-db-all.pl -config test_files/AK58V4MP.txt converting gene format to use-able input done converting gene format making single records file Possible precedence issue with control flow operator at /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm line 791. Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274. Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280. Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274. Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280. Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274. Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280. Use of uninitialized value $aa in string eq at make-single-records-BIOPERL.pl line 274. Use of uninitialized value $aa in concatenation (.) or string at make-single-records-BIOPERL.pl line 280. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $orig_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value $mutated_aa in string eq at make-single-records-BIOPERL.pl line 551. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305. Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.