bio-ontology-research-group / deepsvp Goto Github PK

Hi, this might be a bad issue to post here because it's mainly with AnnotSV I guess, but if you could help it would be much appreciated.

I am getting this error when running annotation.sh:

No SV to annotate in the SVinputFile - Exit without error.

I have tried multiple vcf files to no avail. Thanks.

edit: just to note, the file size of the vcf is not 0.

Hi, I am having a problem while installation.
I followed the steps by creating a conda environment and pip install deepsvp. However, an error throw out:
error in smart_open setup command: 'python_requires' must be a string containing valid version specifiers; Invalid specifier: '>=3.6.*'
After googling, I am not sure how to fix this issue, do you have any suggestions?

Best

Shirley

Hi,

I would like to install DeepSVP with the following command:

conda create -n deepsvp-py38-pip2031 python=3.8 pip=20.3.1
conda activate deepsvp-py38-pip2031
pip3 install deepsvp==1.0.3

but I have this error message:

 ERROR: Command errored out with exit status 1:
     command: /home/wangzh/miniconda3/envs/deepsvp-py38-pip2031/bin/python3.8 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-joadgm7k/smart-open_bb4492a42a8742308626c897d6dcc1fb/setup.py'"'"'; __file__='"'"'/tmp/pip-install-joadgm7k/smart-open_bb4492a42a8742308626c897d6dcc1fb/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-4069swc8
         cwd: /tmp/pip-install-joadgm7k/smart-open_bb4492a42a8742308626c897d6dcc1fb/
    Complete output (1 lines):
    error in smart_open setup command: 'python_requires' must be a string containing valid version specifiers; Invalid specifier: '>=3.6.*'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Thank you for any help you can provide me

Hi,

I would like to install DeepSVP with the following command:

pip3 install deepsvp

but I have this error message:

Collecting tensorflow==2.3.0
  Could not find a version that satisfies the requirement tensorflow==2.3.0 (from versions: 0.12.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.3.0, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.6.0, 1.7.0, 1.7.1, 1.8.0, 1.9.0, 1.10.0, 1.10.1, 1.11.0, 1.12.0, 1.12.2, 1.12.3, 1.13.1, 1.13.2, 1.14.0)
No matching distribution found for tensorflow==2.3.0

Actually, I've had difficulties with the following requirement:

pip3 install tensorflow==2.3.0   
Collecting tensorflow==2.3.0
  Could not find a version that satisfies the requirement tensorflow==2.3.0 (from versions: 0.12.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.3.0, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.6.0, 1.7.0, 1.7.1, 1.8.0, 1.9.0, 1.10.0, 1.10.1, 1.11.0, 1.12.0, 1.12.2, 1.12.3, 1.13.1, 1.13.2, 1.14.0)
No matching distribution found for tensorflow==2.3.0

Thank you for any help you can provide me,
Véronique

Hi @azzatha, How about updating to the lastest AnnotSV version (v3.1)?

Originally posted by @xiucz in #6 (comment)

Hi, am back after calling and annotating CNV.

When running DeepSVP now, I get to 75% and immediately crash to this traceback:

Traceback (most recent call last):
File "/Users/alessihd/opt/miniconda3/envs/py36/bin/deepsvp", line 8, in
sys.exit(main())
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/deepsvp/main.py", line 119, in main
maf_filter)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/deepsvp/main.py", line 290, in func_wrapper
value = func(*args, **kwargs)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/deepsvp/main.py", line 460, in load_cnv_model
data['1000g_AF'].fillna(0, inplace=True)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/pandas/core/frame.py", line 2902, in getitem
indexer = self.columns.get_loc(key)
File "/Users/alessihd/opt/miniconda3/envs/py36/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc
raise KeyError(key) from err
KeyError: '1000g_AF'

This seems to be because my annotated output has no 1000g_AF column. Unfortunately, after further diving into the DeepSVP codebase, almost none of the columns (i.e., NumPromoters, TriS_CGscore) match up with what came from the AnnotSV annotation.

Has AnnotSV changed their labels? Any ideas would be appreciated. Thanks!