classify.pl error: Use of uninitialized value $tgene in substitution (s///)

[dpaudel]

Hello, I am trying to get the Allele.ctg.table. However, I get the following issue while running the classify.pl step on all the lines:

Use of uninitialized value $tgene in substitution (s///) at /apps/allhic/0.9.8/scripts/classify.pl line 54, <IN> line 1.
Use of uninitialized value $tgene in hash element at /apps/allhic/0.9.8/scripts/classify.pl line 55, <IN> line 1.
Use of uninitialized value $tgene in substitution (s///) at /apps/allhic/0.9.8/scripts/classify.pl line 54, <IN> line 2.
Use of uninitialized value $tgene in hash element at /apps/allhic/0.9.8/scripts/classify.pl line 55, <IN> line 2.
Use of uninitialized value $tgene in substitution (s///) at /apps/allhic/0.9.8/scripts/classify.pl line 54, <IN> line 3.

My blast file looks like this:

g3.t1   Ra_g10985.t1    97.158  563     16      0       328     890     223     785     0.0     952
g5.t1   Ra_g10987.t1    98.725  1725    22      0       1       1725    1       1725    0.0     3064

The reference gff file looks like this:

Ra01    BRAKER  gene    982     8080    1       -       .       ID=Ra_g1;
Ra01    BRAKER  mRNA    982     8080    1       -       .       ID=Ra_g1.t1;Parent=Ra_g1;
Ra01    BRAKER  stop_codon      982     984     .       -       0       ID=Ra_g1.t1.stop1;Parent=Ra_g1.t1;

The query gff looks like this:

203     AUGUSTUS        gene    23237   25005   0.64    -       .       ID=g1;
203     AUGUSTUS        mRNA    23237   25005   0.64    -       .       ID=g1.t1;Parent=g1;
203     AUGUSTUS        stop_codon      23237   23239   .       -       0       ID=g1.t1.stop1;Parent=g1.t1;

Could you please check? Thanks -Dev

[tangerzhang]

Hi @dpaudel You can modify the script in Lines 53 and 65, and change the string 'Name=' to 'ID=' It is supposed to solve this problem. Thanks!