No gene and PAV has overlap warning while constructing pangenome

Question

[analyst]

Dear all,

I am trying to construct pangenome for example data; genomes provided in psvcp_v1.01-main pipeline using script "1Genome_construct_Pangenome.py" but it generates warning of "No gene and PAV has overlap, next round".

Please guide if i am using right approach to construct linear pangenome as i have to construct linear pangenome for my dataset later on.

Thanks

Command: python3 ../1Genome_construct_Pangenome.py genome_gff_dir_example/ genome_list

1 nucmer ok
2 Assemblytics ok
index file pan_dir_result/ref0.fa.fai not found, generating...
3 final.bed ok
4 more_50.bed ok
/home/nigab/Documents/Bushra/Dr_Ramzan_Aamir/psvcp_v1.01-main/example7/../construct_pan_script/5ins.bed_to_bed2.py:9: SyntaxWarning: invalid escape sequence '\S'
  qstart = re.findall('(.+?)_(C.+?):(\S+?)-',one_line_list[8])
5 more_50.bed2 ok
/home/nigab/Documents/Bushra/Dr_Ramzan_Aamir/psvcp_v1.01-main/example7/../construct_pan_script/6update_ref_by_nucmer.py:19: SyntaxWarning: invalid escape sequence '\s'
  df = pd.read_csv(sys.argv[2],sep="\s+",header=None)
6 6update_ref_by_nucmer.py ok
7 7bed2_update_bed3.R ok
7.2 7.2bed3_to_gff.py ok
8 8gff_update_by_bed2info_parLapply.R ok
9 9gff_split_by_bed3_5.R ok
No gene and PAV has overlap, next round
1 nucmer ok
2 Assemblytics ok
index file pan_dir_result/ref1.fa.fai not found, generating...
3 final.bed ok
4 more_50.bed ok
ins.more_50.bed is empty
next round
1 nucmer ok
2 Assemblytics ok
index file pan_dir_result/ref2.fa.fai not found, generating...
3 final.bed ok
4 more_50.bed ok
/home/nigab/Documents/Bushra/Dr_Ramzan_Aamir/psvcp_v1.01-main/example7/../construct_pan_script/5ins.bed_to_bed2.py:9: SyntaxWarning: invalid escape sequence '\S'
  qstart = re.findall('(.+?)_(C.+?):(\S+?)-',one_line_list[8])
5 more_50.bed2 ok
/home/nigab/Documents/Bushra/Dr_Ramzan_Aamir/psvcp_v1.01-main/example7/../construct_pan_script/6update_ref_by_nucmer.py:19: SyntaxWarning: invalid escape sequence '\s'
  df = pd.read_csv(sys.argv[2],sep="\s+",header=None)
6 6update_ref_by_nucmer.py ok
7 7bed2_update_bed3.R ok
7.2 7.2bed3_to_gff.py ok
8 8gff_update_by_bed2info_parLapply.R ok
9 9gff_split_by_bed3_5.R ok
10 10gene_in_pv_from_gff_parLapply2.R ok; Gene, exon, CDS ... have overlap with PAV 
No gene loactes in PAV absolutly, next round
1 nucmer ok
2 Assemblytics ok
index file pan_dir_result/ref3.fa.fai not found, generating...
3 final.bed ok
4 more_50.bed ok
/home/nigab/Documents/Bushra/Dr_Ramzan_Aamir/psvcp_v1.01-main/example7/../construct_pan_script/5ins.bed_to_bed2.py:9: SyntaxWarning: invalid escape sequence '\S'
  qstart = re.findall('(.+?)_(C.+?):(\S+?)-',one_line_list[8])
5 more_50.bed2 ok
/home/nigab/Documents/Bushra/Dr_Ramzan_Aamir/psvcp_v1.01-main/example7/../construct_pan_script/6update_ref_by_nucmer.py:19: SyntaxWarning: invalid escape sequence '\s'
  df = pd.read_csv(sys.argv[2],sep="\s+",header=None)
6 6update_ref_by_nucmer.py ok
7 7bed2_update_bed3.R ok
7.2 7.2bed3_to_gff.py ok
8 8gff_update_by_bed2info_parLapply.R ok
9 9gff_split_by_bed3_5.R ok
No gene and PAV has overlap, next round