Run error
gpcr opened this issue · 4 comments
Command-line used to cause the issue
swiss --assoc test_hg19.gz --ld-clump --clump-p 5e-06 --out my_results
swiss --assoc file.txt ...
Path to your data (if publicly available)
Problem description
Please describe the issue:
aborted with below error message
- What is the problem?
- Is it reproducible?
- What was the expected output?
Program output
- What did the program output? Was there an error message?
Traceback (most recent call last):
File "/usr/local/bin/swiss", line 20, in
main()
File "/usr/local/lib/python2.7/dist-packages/swiss/main.py", line 962, in main
(opts,args) = get_settings(arg_string)
File "/usr/local/lib/python2.7/dist-packages/swiss/main.py", line 544, in get_settings
check_plink_version(opts.plink_path)
File "/usr/local/lib/python2.7/dist-packages/swiss/main.py", line 286, in check_plink_version
x, y, beta, z = re.search("v(\d+).(\d+)b?(\d+)?.(\w+)",version_string).groups()
AttributeError: 'NoneType' object has no attribute 'groups'
Swiss version
1.0b4
plink --version
PLINK v1.90b5 64-bit (14 Nov 2017)
If you don't know your swiss version, please do:
swiss --versionLooks like a bug that was fixed earlier this year (#7). Try updating to the latest version and see if you still see the same error.
Now I get this error
$ swiss --assoc test_hg19.gz --ld-clump --clump-p 5e-06 --out my_results
+-----------------------------------+
| Swiss - 1.0.0 |
+-----------------------------------+
| Ryan Welch (welchr@umich.edu) |
+-----------------------------------+
| https://github.com/welchr/Swiss |
+-----------------------------------+
Loading results file: test_hg19.gz
Traceback (most recent call last):
File "/usr/local/bin/swiss", line 20, in
main()
File "/usr/local/lib/python2.7/dist-packages/swiss/main.py", line 1064, in main
run_process(opts.assoc,opts.trait,opts.out,opts)
File "/usr/local/lib/python2.7/dist-packages/swiss/main.py", line 791, in run_process
results.load(sep=opts.delim)
File "/usr/local/lib/python2.7/dist-packages/swiss/AssocResults.py", line 157, in load
chunk = chunk[chunk[self.pval_col] < self.pval_thresh]
File "/usr/local/lib/python2.7/dist-packages/pandas/core/frame.py", line 2139, in getitem
return self._getitem_column(key)
File "/usr/local/lib/python2.7/dist-packages/pandas/core/frame.py", line 2146, in _getitem_column
return self._get_item_cache(key)
File "/usr/local/lib/python2.7/dist-packages/pandas/core/generic.py", line 1842, in _get_item_cache
values = self._data.get(item)
File "/usr/local/lib/python2.7/dist-packages/pandas/core/internals.py", line 3843, in get
loc = self.items.get_loc(item)
File "/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/base.py", line 2527, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 117, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 139, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1265, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1273, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'PVALUE'
If that's the same test_hg19.gz from the test directory, you can look at the tests to see the various command lines used:
Lines 39 to 43 in 9ae335a
That particular file is in "multi-assoc" format, where there are multiple p-value and effect size columns, one set per trait tested.
yes, same file from the test folder
Thanks!!!!
Working fine with below command
swiss --assoc test_hg19.gz --multi-assoc --build hg19 --ld-clump-source 1000G_2014-11_ALL --ld-gwas-source 1000G_2014-11_ALL --gwas-cat gwascat_ebi_GRCh37p13.tab --ld-clump --clump-p 5e-06 --out my_results