about pan-genome analysis

[sunnycqcn]

Hello,
Much appreciated for your excellent work.
I try to run your code in my project with pangenome command.
I met a error as following:
Starting ====== 2020-02-27 12:40:48 ======
Traceback (most recent call last):
File "/isilon/saskatoon-rdc/users/fuf/comDIR/AMPRIL-genomes/pangenome/wga.pangenome.py", line 236, in
main(sys.argv[1:])
File "/isilon/saskatoon-rdc/users/fuf/comDIR/AMPRIL-genomes/pangenome/wga.pangenome.py", line 52, in main
result = runJob(arr, num, chrBeds, accs, wgadir, outdir)
File "/isilon/saskatoon-rdc/users/fuf/comDIR/AMPRIL-genomes/pangenome/wga.pangenome.py", line 91, in runJob
t = getLen(chrBeds[accs[j]])
File "/isilon/saskatoon-rdc/users/fuf/comDIR/AMPRIL-genomes/pangenome/wga.pangenome.py", line 217, in getLen
fi = open(inFile,"r")
IOError: [Errno 2] No such file or directory: './chrsize/C24.leng.txt'
###########################################################################
So can I use your code in my project? Because I check the command and find you have difined the accs as following:
accs = ["An-1","C24","Col","Cvi","Eri","Kyo","Ler","Sha"].
I think this is only for your project.
Thanks,
Fuyou

[wen-biao]

Hi Fuyou,

the error message shows you need a genome length file for each genome, this tab-formated file like below
chr1 25332333
chr2 192012013
...
chrN 29139132

the script should be OK for other pan-genome project after changing some lines accordingly.

[sunnycqcn]

Hello Wen-Biao,
I got the tab-formated file and changed the accs to my name. The code works well. But I still have a little question about the files from "all pairwise whole genome comparisons using MUMmer".
When I run the changed command wga.pangenome.py, I get error as following:
cat: ./genome/L002/L003/L003.del.bed: No such file or directory
cat: ./genome/L003/L002/L002.del.bed: No such file or directory
cat: ./genome/L002/L003/L003.wga.block.txt: No such file or directory
cat: ./genome/L003/L002/L002.wga.block.txt: No such file or directory
These pairwise files are generated by command "syri -c out.chrom.coords -d out_m_i90_l100.delta -r Col.fasta -q An-1.fasta --nc 5 --all -k".
Or we have to use mummer to generate them. If by ourself, could you tell me the format?
Thanks,
Fuyou

[liufy11]

I run the pangenome script smoothly. in my opinion , you should create the above files by yourself. look at README.md under AMPRIL-genomes/pangenome