error when run example!

[scotty323]

make_pan.pl --ref Zmw_sc00394.1.fa --ref_anno Zmw_sc00394.1.gff3 --query Zjn_sc00188.1.fa --query_anno Zjn_sc00188.1.gff3
中间省略

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!

BUT, I think the result " pangenome1.fa" is wrong:

AAATTATATTAGTAGATTTATCATGTAATAAATTTTCATATTATGTAATTTTTAATATTAAATTTTTTTAAATATTATTA
GTCAATGTTAAAAAAATTTGACTTTGACCAAAATCAGGAATGTTTATATTTTGGGAAGGGGTTAGTATAAAGTTTGTGAG
GAATAAACCTAGGGATTCGAGATTACATGAATTCCAAGCAAGGGCCCGCCGGCAGGCATGCAATGCAAGAGGCGGAGGCC
CGGTGTGCTTCATGGATTAGCCATGCAGGCTTTTGGAGAAAAGCCGTGGGCATGCAGCGAATTAATGCAGCCAAAATTGC

Zjn_sc00188.1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

So any solution?

[liufy11]

Hello scotty323 !
I meet with the same question with you. Have you solve it ? Why do you think the result " pangenome1.fa" is wrong ?

[Zhuxitong]

Sorry for a late reply.

This peoblem shoud derive from that bedtools getfasta bug. I downloaded it very long time ago and I could use standout as output, like bedtools getfasta ... > output. However recently with same version of bedtools, it requires -fo as output, which means bedtools getfasta ... -fo output. If you use the recent version of bedtools, you would like to get a empty output file and then meet the problem in get_the_pav_seq.pl. So download ppsPCP again and try again.