{"action":"opened","issue":{"url":"https://api.github.com/repos/msettles/dbcAmplicons/issues/40","repository_url":"https://api.github.com/repos/msettles/dbcAmplicons","labels_url":"https://api.github.com/repos/msettles/dbcAmplicons/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/msettles/dbcAmplicons/issues/40/comments","events_url":"https://api.github.com/repos/msettles/dbcAmplicons/issues/40/events","html_url":"https://github.com/msettles/dbcAmplicons/issues/40","id":356933893,"node_id":"MDU6SXNzdWUzNTY5MzM4OTM=","number":40,"title":"abundance step appears to run but output files are empty","user":{"login":"rpduncan","id":1068469,"node_id":"MDQ6VXNlcjEwNjg0Njk=","avatar_url":"https://avatars3.githubusercontent.com/u/1068469?v=4","gravatar_id":"","url":"https://api.github.com/users/rpduncan","html_url":"https://github.com/rpduncan","followers_url":"https://api.github.com/users/rpduncan/followers","following_url":"https://api.github.com/users/rpduncan/following{/other_user}","gists_url":"https://api.github.com/users/rpduncan/gists{/gist_id}","starred_url":"https://api.github.com/users/rpduncan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rpduncan/subscriptions","organizations_url":"https://api.github.com/users/rpduncan/orgs","repos_url":"https://api.github.com/users/rpduncan/repos","events_url":"https://api.github.com/users/rpduncan/events{/privacy}","received_events_url":"https://api.github.com/users/rpduncan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-04T18:53:46Z","updated_at":"2018-09-04T18:53:46Z","closed_at":null,"author_association":"NONE","body":"Hello! I've gotten almost all the way through the pipeline with no problem until the abundance step. When I run:\r\n\r\n`dbcAmplicons abundance -S SampleSheet.txt -O test-results/16sV4 -F NWRD001_1.classified.fixrank --biom > abundance.16sV4.log\r\n`\r\nI get this output, but all of my output files are empty. I checked with the HPC support people at my institution and they said that the error messages about numPy were safe to ignore:\r\n\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._ufuncs import *lines, 44403.0 lines/second\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._solve_toeplitz import levinsonlines/second\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._decomp_update import *\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from . import _bspl\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from . import _csparsetools\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\\\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._tools import csgraph_to_dense, csgraph_from_dense,\\\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._traversal import breadth_first_order, depth_first_order, \\\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._min_spanning_tree import minimum_spanning_tree\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \\\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from .ckdtree import *\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from .qhull import *\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from . import _voronoi\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from . import _hausdorff\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._trlib import TRLIBQuadraticSubproblem\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from ._group_columns import group_dense, group_sparse\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from . import _stats\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import (hashtable as _hashtable,\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import algos, lib\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import hashing, tslib\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import (lib, index as libindex, tslib as libts,\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  import pandas._libs.tslibs.offsets as liboffsets\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import algos as libalgos, ops as libops\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs.interval import (\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import internals as libinternals\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  import pandas._libs.sparse as splib\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  import pandas._libs.window as _window\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import (lib, reduction,\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import algos as _algos, reshape as _reshape\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  import pandas._libs.parsers as parsers\r\n/global/home/users/rpduncan/src/dbcA_virtualenv/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\r\n  from pandas._libs import algos, lib, writers as libwriters\r\nprocessed 100000 total lines, 38930.0 lines/second\r\nprocessed 200000 total lines, 41795.0 lines/second\r\nprocessed 300000 total lines, 42559.0 lines/second\r\nprocessed 400000 total lines, 43132.0 lines/second\r\nprocessed 500000 total lines, 43520.0 lines/second\r\nprocessed 600000 total lines, 43753.0 lines/second\r\nprocessed 700000 total lines, 43928.0 lines/second\r\nprocessed 800000 total lines, 44070.0 lines/second\r\nprocessed 900000 total lines, 44183.0 lines/second\r\nprocessed 1000000 total lines, 44272.0 lines/second\r\nprocessed 1100000 total lines, 44343.0 lines/second\r\nprocessed 1200000 total lines, 44403.0 lines/second\r\nprocessed 1300000 total lines, 44431.0 lines/second\r\nprocessed 1400000 total lines, 44371.0 lines/second\r\nprocessed 1500000 total lines, 44361.0 lines/second\r\nWriting output\r\nWriting json formatted biom file to: results/16sV4.biom\r\nWriting abundance file to: results/16sV4.abundance.txt\r\nWriting proportions file to: results/16sV4.proportions.txt\r\nfinished in 0.57 minutes\r\nCleaning up."}}
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