mnshgl0110
commented
1 year ago The order of genomes in genomes.txt need to match the order in which the syri output is provided. From the README:
NOTE: It is required that the order of the genomes is the same as the order in which genomes are compared. For example, if the first genome annotation file uses A as a reference and B as query, and the second genome annotation file uses B as a reference and C as query, then the genomes.txt file should list the genomes in the order A, B, C.Please check that your input files and genome order are consistent.
This my genome.txt file,but when I run plotsr ,then bollow
file name tags
1C32_ragtag.fa 1C32 lw:1.5 GCA_000400815.2_ragtag.fa GCA_000400815.2 lw:1.5 GCA_000952015.1_ragtag.fa GCA_000952015.1 lw:1.5 GCA_018140845.1_ragtag.fa GCA_018140845.1 lw:1.5 GCA_018440705.1_ragtag.fa GCA_018440705.1 lw:1.5
/public/home/yqming/miniconda3/envs/syri/bin/plotsr:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import('pkg_resources').run_script('plotsr==1.1.2', 'plotsr') 2023-11-22 12:30:26,241 - Plotsr - INFO - Starting Traceback (most recent call last): File "/public/home/yqming/miniconda3/envs/syri/bin/plotsr", line 4, in
import('pkg_resources').run_script('plotsr==1.1.2', 'plotsr')
File "/public/home/yqming/miniconda3/envs/syri/lib/python3.9/site-packages/pkg_resources/init.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/public/home/yqming/miniconda3/envs/syri/lib/python3.9/site-packages/pkg_resources/init.py", line 1572, in run_script
exec(script_code, namespace, namespace)
File "/public/home/yqming/miniconda3/envs/syri/lib/python3.9/site-packages/plotsr-1.1.2-py3.9.egg/EGG-INFO/scripts/plotsr", line 6, in
File "/public/home/yqming/miniconda3/envs/syri/lib/python3.9/site-packages/plotsr-1.1.2-py3.9.egg/plotsr/scripts/plotsr.py", line 334, in main
File "/public/home/yqming/miniconda3/envs/syri/lib/python3.9/site-packages/plotsr-1.1.2-py3.9.egg/plotsr/scripts/plotsr.py", line 171, in plotsr
File "/public/home/yqming/miniconda3/envs/syri/lib/python3.9/site-packages/plotsr-1.1.2-py3.9.egg/plotsr/scripts/func.py", line 1050, in validalign2fasta
ImportError: For chromosome ID: Hic3, length in genome fasta: genome.txt is less than the maximum coordinate in the structural annotation file: syri.out. Exiting.
why is Hic3 very too long ? How to solve this strange problem?