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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
74 stars 17 forks source link

Annotate with CADD not working #33

Closed landyk01 closed 9 years ago

landyk01 commented 9 years ago

I am trying to annotate a vcf file with the 1000G CADD score file as follows:

genmod annotate example/test.vcf --cadd_1000g example/1000G.tsv.gz -o example/test.annotated.vcf

I receive the following messages: (minerva is the name of the supercomputer where genmod is installed as a python package)

The HPC help desk that services the supercomputer was not able to resolve the problem and believes there is something wrong with genmod, as other annotations without CADD files work well.

Any help would greatly appreciated!

Traceback (most recent call last): File "/hpc/packages/minerva-common/py_packages/2.7/bin/genmod", line 70, in run_genmod() File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/site-packages/click/core.py", line 610, in call return self.main(_args, _kwargs) File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/site-packages/click/core.py", line 590, in main rv = self.invoke(ctx) File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/site-packages/click/core.py", line 936, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/site-packages/click/core.py", line 782, in invoke return ctx.invoke(self.callback, _ctx.params) File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/site-packages/click/core.py", line 416, in invoke return callback(_args, **kwargs) File "/hpc/packages/minerva-common/py_packages/2.7/lib/python2.7/site-packages/genmod/commands/annotate.py", line 386, in annotate individuals, UnboundLocalError: local variable 'individuals' referenced before assignment Process VariantPrinter-10: Traceback (most recent call last): File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/hpc/packages/minerva-common/py_packages/2.7/lib/python2.7/site-packages/genmod/variant_printer.py", line 42, in run next_result = self.task_queue.get() File "", line 2, in get File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/multiprocessing/managers.py", line 755, in _callmethod self._connect() File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/multiprocessing/managers.py", line 743, in _connect dispatch(conn, None, 'accept_connection', (name,)) File "/hpc/packages/minerva-common/python/2.7.6/lib/python2.7/multiprocessing/managers.py", line 102, in dispatch kind, result = c.recv() IOError: [Errno 104] Connection reset by peer

moonso commented 9 years ago

Thank you for spotting this one. It is fixed in version 1.8.2!