plostr error

[zhangxn-flower]

hi, I'm running syri for analysis of genomes.
syri --version
1.5.4
python3 $PATH_TO_PLOTSR
usage: Plotting structural rearrangements between genomes [-h] [--sr SR] [--bp BP] --genomes GENOMES [--markers MARKERS] [--tracks TRACKS] [--chrord CHRORD] [--chrname CHRNAME] [-o O] [--itx] [--chr CHR] [--reg REG] [--rtr] [--nosyn] [--noinv] [--notr] [--nodup] [-s S] [--cfg CFG] [-R] [-f F] [-H H] [-W W] [-S S] [-d D] [-b {agg,cairo,pdf,pgf,ps,svg,template}] [-v] [--log {DEBUG,INFO,WARN}] [--version]

command line is like this :
python3 $PATH_TO_PLOTSR --sr syri.out --genomes genomes
cat genomes
/home A.chr.fa refgenome
/home B.chr.fa refgenome

but the error appear.
ImportError: Incomplete genomic information.
Expected format for the genome file:
path_to_genome1 genome1_id tags
path_to_genome2 genome2_id tags

Make sure that the columns are separated by tabs (and not spaces).
so, what should be the format of the input file --genomes
Could you please guide if there is any solution, how to fix theproblem?

Many thanks,
xn

[mnshgl0110]

Hi Xn,
In the genomes.txt file, the first column needs to be the complete path to the .fa/.chrlen files whereas the second column should be genome-name. So, in this case, your genomes.txt file would look like:

/home/A.chr.fa refgenome
/home/B.chr.fa qrygenome

Also, make sure that the columns are separated by tab (and not spaces).

Best
Manish

P.S.: It is more helpful if the questions for a repo (here plotsr) is asked in that repo only as it allows future users facing the same issue to find the solution quickly.

[TZM9882]

hello Manih,

I am very new to this whole process but still trying my best using manuals and similar issues by previous users. Thanks to those unknown users.

I also got below the error for plotsr. I followed the instructions.
Am I still wrong somewhere?
Image 2 is how I prepared genomes.txt for 2 genomes (A is reference).
Please help me with this problem

Thanks,
Mg