程序报错

[ysy12306]

我运行的每组数据都会出现
“substr outside of string at PGA.pl line 5475.
substr outside of string at PGA.pl line 7831.”的提示，请问这是程序存在问题吗，是否会影响结果

[quxiaojian]

我运行的每组数据都会出现 “substr outside of string at PGA.pl line 5475. substr outside of string at PGA.pl line 7831.”的提示，请问这是程序存在问题吗，是否会影响结果

示例也会出现这个吗？

[ysy12306]

示例不会，我分析的是拟南芥叶绿体，运行后警告中还有这些信息：
Warning: trnA (positive one-intron PCG) intron-exon boundary need to be checked!
Warning: trnG (positive one-intron PCG) has non-canonical start codon and intron-exon boundary need to be checked!
Warning: trnI (positive one-intron PCG) intron-exon boundary need to be checked!
Warning: trnK (negative one-intron PCG) has non-canonical start codon and intron-exon boundary need to be checked!
Warning: trnL (positive one-intron PCG) intron-exon boundary need to be checked!
Total number of genes in the reference plastome(s): 131.
Total number of genes annotated in the target plastome: 112.
All gene names from the reference plastome(s) that were not annotated in the target plastome:
trnW trnD trnM trnfM rrn5S trnN trnP trnY trnE trnF trnQ trnS trnT rrn23S rrn16S trnH trnC rrn5s rrn4.5S

[quxiaojian]

示例不会，我分析的是拟南芥叶绿体，运行后警告中还有这些信息： Warning: trnA (positive one-intron PCG) intron-exon boundary need to be checked! Warning: trnG (positive one-intron PCG) has non-canonical start codon and intron-exon boundary need to be checked! Warning: trnI (positive one-intron PCG) intron-exon boundary need to be checked! Warning: trnK (negative one-intron PCG) has non-canonical start codon and intron-exon boundary need to be checked! Warning: trnL (positive one-intron PCG) intron-exon boundary need to be checked! Total number of genes in the reference plastome(s): 131. Total number of genes annotated in the target plastome: 112. All gene names from the reference plastome(s) that were not annotated in the target plastome: trnW trnD trnM trnfM rrn5S trnN trnP trnY trnE trnF trnQ trnS trnT rrn23S rrn16S trnH trnC rrn5s rrn4.5S

不要随意改变参考，用无油樟即可。如果想用其它物种作为参考，请先用无油樟作为参考注释其它物种，保证参考的准确性