Bio::Root::Exception <<Bad end parameter (270015). End must be less than the total length of sequence (total=160554)

[Github-Yilei]

No description provided.

[Github-Yilei]

Hi, Mr. Zhu.

Thank you for building the ppsPCP workflow, and it is working well with the example. But when I performing it with my data, there is an "ERROR" at get_pav_for_each.pl:

Step 6: Filtering and annotating genes overlapped with extracted PAVs!

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bad end parameter. End must be less than the total length of sequence
STACK: Error::throw
STACK: Bio::Root::Root::throw miniconda3/pkgs/perl-bioperl-core-1.007002-pl526_2/lib/site_perl/5.26.2//Bio/Root/Root.pm:447
STACK: Bio::PrimarySeq::subseq miniconda3/pkgs/perl-bioperl-core-1.007002-pl526_2/lib/site_perl/5.26.2//Bio/PrimarySeq.pm:452
STACK: Bio::Seq::subseq miniconda3/pkgs/perl-bioperl-core-1.007002-pl526_2/lib/site_perl/5.26.2//Bio/Seq.pm:630
STACK: biosoft/ppsPCP_file/ppsPCP/bin/../src/get_pav_for_each.pl:71

the versions of the packages are according to manuls, I can't find a way to solve this problem, Any help would be greatly appreciated.

[Github-Yilei]

I find that the end parameter (270015) belongs to contig100 at seq_pav_region.txt, on the other hand, the total length of the sequence (total=160554) is the length of contig101.

[Zhuxitong]

@Github-Yilei Do you finally fix it? This error rarely happens.

[Github-Yilei]

Hi, Mr. @Zhuxitong.

The script get_pav_for_each.pl will return the Location of the previous gene at the end of ${querybase}_pav_intersect_gene.gff3. It may results in the error above while the final lines of ${querybase}_pav_intersect_gene.gff3 is unique and $pretmp[3]>=$arrtmp[0].

I would like to pull a request, place to make sure if the script makes sense.

Thanks.

[Zhuxitong]

OK, @Github-Yilei I will check it once I am free.