Error in step 4: invalid literal for int() with base 10: 'https://git-lfs.github.com/spec/v1'

[YiweiNiu]

Hi,

I got an error in step 4, and the following were the error message:

Step4: Resolving structure ... 
Traceback (most recent call last):
  File "/home/work01/.local/bin/svelter.py", line 4, in <module>
    __import__('pkg_resources').run_script('SVelter==1.1.0', 'svelter.py')
  File "/home/work01/tools/python2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 738, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/work01/tools/python2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1506, in run_script
    exec(script_code, namespace, namespace)
  File "/home/work01/.local/lib/python2.7/site-packages/SVelter-1.1.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/svelter.py", line 4221, in <module>
    
  File "/home/work01/.local/lib/python2.7/site-packages/SVelter-1.1.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/svelter.py", line 3412, in global_para_declaration
    
  File "svelter_sv/function.pyx", line 1513, in svelter_sv.function.GC_Index_Readin
ValueError: invalid literal for int() with base 10: 'https://git-lfs.github.com/spec/v1'
svelter/bp_files.6792D.marked.bam/6792D.marked.chr10.txt done!
Traceback (most recent call last):
  File "/home/work01/.local/bin/svelter.py", line 4, in <module>
    __import__('pkg_resources').run_script('SVelter==1.1.0', 'svelter.py')
  File "/home/work01/tools/python2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 738, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/work01/tools/python2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1506, in run_script
    exec(script_code, namespace, namespace)
  File "/home/work01/.local/lib/python2.7/site-packages/SVelter-1.1.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/svelter.py", line 4221, in <module>

The bam I used was produced by bwa mem. The Python version is 2.7.13.

Do you know how to solve this? Thanks!

Yiwei Niu

[kelvin-tran]

In case anyone else comes across this, I think the issue is that the file is tracked by git-lfs, and therefore is just a pointer, so when you try to use the file, instead of the correct value, you get the pointer, and hence the ValueError.

If this is the case, solution is to install git lfs.