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csv Error: field larger than field limit (131072) #4

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george-githinji opened this issue Sep 28, 2020 · 0 comments
Open

csv Error: field larger than field limit (131072) #4

george-githinji opened this issue Sep 28, 2020 · 0 comments

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@george-githinji
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george-githinji commented Sep 28, 2020

I seem to be running into this issue with llama on an Ubuntu 18 machine

Traceback (most recent call last):
  File "/home/tiba01/anaconda3/envs/llama/bin/find_ambiguities.py", line 4, in <module>
    __import__('pkg_resources').run_script('llama==0.1', 'find_ambiguities.py')
  File "/home/tiba01/anaconda3/envs/llama/lib/python3.6/site-packages/pkg_resources/__init__.py", line 665, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/tiba01/anaconda3/envs/llama/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1463, in run_script
    exec(code, namespace, namespace)
  File "/home/tiba01/anaconda3/envs/llama/lib/python3.6/site-packages/llama-0.1-py3.6.egg/EGG-INFO/scripts/find_ambiguities.py", line 62, in <module>
    find_snps()
  File "/home/tiba01/anaconda3/envs/llama/lib/python3.6/site-packages/llama-0.1-py3.6.egg/EGG-INFO/scripts/find_ambiguities.py", line 37, in find_snps
    for row in reader:
  File "/home/tiba01/anaconda3/envs/llama/lib/python3.6/csv.py", line 112, in __next__
    row = next(self.reader)
_csv.Error: field larger than field limit (131072)

Error in rule ambiguities_at_snp_sites:
 .
.
.
.
Exiting because a job execution failed. Look above for error message

seems like this is a common issue:
field size larger than field limit

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