merge tissue

[ChenDepp]

hello brentp! when i merge the vcf file,it report the error ,can you tell me how to solve it? thank your

[brentp]

that error is indicating that your numpy installation is broken. can you show the full error in text, not image?

[ChenDepp]

root@b66aec3f537b:/store/gchen/smoove# smoove merge --name merged --outdir ../results/ -f GDDH13_1-1_formatted.fasta ../results/.genotyped.vcf.gz [smoove] 2019/06/14 02:02:39 starting with version 0.2.3 [smoove] 2019/06/14 02:02:39 merging 209 files [smoove] 2019/06/14 02:02:39 finished sorting 209 files; merge starting. [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/special/init.py:640: RuntimeWarning: nu mpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._ufuncs import [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.d type size changed, may indicate binary incompatibility. Expected 96, got 88 from ._solve_toeplitz import levinson [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/linalg/init.py:207: RuntimeWarning: num py.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._decomp_update import [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: n umpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning : numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from . import _bspl [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dty pe size changed, may indicate binary incompatibility. Expected 96, got 88 from . import _csparsetools [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:165: RuntimeWarn ing: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\ [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWar ning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._tools import csgraph_to_dense, csgraph_from_dense,\ [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:167: RuntimeWarn ing: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._traversal import breadth_first_order, depth_first_order, \ [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:169: RuntimeWarn ing: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._min_spanning_tree import minimum_spanning_tree [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:170: RuntimeWarn ing: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \ [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/spatial/init.py:95: RuntimeWarning: num py.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from .ckdtree import [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/spatial/init.py:96: RuntimeWarning: num py.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from .qhull import * [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWa rning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from . import _voronoi [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/spatial/distance.py:122: RuntimeWarning: nu mpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from . import _hausdorff [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/optimize/_trlib/init.py:1: RuntimeWarni ng: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._trlib import TRLIBQuadraticSubproblem [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: nu mpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._group_columns import group_dense, group_sparse [smoove] 2019/06/14 02:02:40 /usr/local/lib/python2.7/dist-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarn ing: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from . import _stats

may is scipy problem?

[ChenDepp]

hello brentp, can i uninstall numpy,and reinstall it?

[brentp]

yes, you can try that. google that error.

[ChenDepp]

@brentp ,thank your help very much!,it running successfully!

[brentp]

glad to hear it.