Error when run the example data!!!

[Boer223]

Hi, Dr.Zhu !

When I run the example data with the ppsPCP, I got this error:

Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,

line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Use of uninitialized value in concatenation (.) or string at /home/tao/ppsPCP/bin/../src/get_the_pav_seq.pl line 33,
line 8.
Number of Zjn_sc00188.1 PAVs added to the pan-genome1: 8
Number of Zjn_sc00188.1 genes added to the pan-genome1: 12
Average length of Zjn_sc00188.1 PAVs: 24.021Kb
Total size of the pan-genome1: 210K
Total number of genes in the pan-genome1: 39
Job successfully completed. Check current directory for final results!

Besides, the output fasta file pan-genome1.fa was added the wrong NNNNNNNNNN sequences.

So, what's the wrong with the ppsPCP tools? Can you give any suggestions?

[Zhuxitong]

Sorry for a late reply.

Have you checked your perl version? Or the bedtools getfasta command in the ppsPCP.sh file to use -fo as output instead of standout. Several months ago I fixed the second problem and update the package. Please check these two requiremets.