These are chat archives for dereneaton/ipyrad

24th
Jan 2019
Tim Böhnert
@TimBoeh
Jan 24 08:28
@eaton-lab Hi Deren, this is the output of conda list ipyrad:
# packages in environment at /home/*user*/miniconda2:
#
# Name                    Version                   Build  Channel
ipyrad                    0.7.29                   py27_0    ipyrad
Tim Böhnert
@TimBoeh
Jan 24 09:07

@eaton-lab oh boy ... now I am getting an even longer error:

## imports
import ipyrad as ip
import ipyrad.analysis as ipa
import ipyparallel as ipp

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-a99cabc2dd5b> in <module>()
      1 ## imports
----> 2 import ipyrad as ip
      3 import ipyrad.analysis as ipa
      4 import ipyparallel as ipp

/home/boehnert/miniconda2/lib/python2.7/site-packages/ipyrad/__init__.pyc in <module>()
     18 
     19 ## main ip.functions
---> 20 from . import load as _load
     21 from . import assemble
     22 from ipyrad.core.parallel import get_client as _get_client

/home/boehnert/miniconda2/lib/python2.7/site-packages/ipyrad/load/__init__.py in <module>()
     12 ""
     13 
---> 14 from .load import test_assembly
     15 from .load import save_json
     16 from .load import load_json

/home/boehnert/miniconda2/lib/python2.7/site-packages/ipyrad/load/load.py in <module>()
     12 import ipyrad as ip
     13 from copy import deepcopy
---> 14 from ipyrad.assemble.util import IPyradWarningExit, ObjDict
     15 from collections import OrderedDict
     16 

/home/boehnert/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/__init__.py in <module>()
      5 from . import demultiplex
      6 from . import rawedit
----> 7 from . import cluster_within
      8 from . import jointestimate
      9 from . import consens_se

/home/boehnert/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_within.py in <module>()
     30 import ipyparallel as ipp
     31 
---> 32 from refmap import *
     33 from util import *
     34 

/home/boehnert/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/refmap.py in <module>()
     13 import glob
     14 import shutil
---> 15 import pysam
     16 import ipyrad
     17 import numpy as np

/home/boehnert/miniconda2/lib/python2.7/site-packages/pysam/__init__.py in <module>()
      3 import sysconfig
      4 
----> 5 from pysam.libchtslib import *
      6 from pysam.libcutils import *
      7 import pysam.libcutils as libcutils

ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Sorry for the long post but I thought those informations might be useful. I tried to find information regarding this mysterious libcrypto.so.1.0.0 but it remains cryptic for me.
After I run the first three importcommand again I get the same error as in the first post.
Cheers, Tim

jhoepke
@jhoepke
Jan 24 14:14
@isaacovercast I observed a strange behaviour: Then I installed ipyrad 0.7.28 in a clean conda environment I got the error "error in filter_stacks on chunk 0: ValueError(zero-size array to reduction operation minimum which has no identity)" but then I installed ipyrad 0.7.28 in a conda environment that is a clone of the root environment there is NO error?! Info: I took the conda root environment from a Miniconda Installation that was used the "Miniconda2-4.0.5-Linux-x86_64.sh" installer and that was updated to conda version 4.3.30 before.
This conda env (a root clone with ipyrad 0.7.28 installed on top) WORKED:
alabaster 0.7.12 py27_0
asn1crypto 0.22.0 py27_0
babel 2.6.0 py27_0
backports 1.0 py27_1
backports.shutil_get_terminal_size 1.0.0 py27_2
backports_abc 0.5 py27_0
blas 1.0 mkl
bleach 3.1.0 py27_0
bokeh 0.13.0 py27_0
certifi 2018.11.29 py27_0
cffi 1.10.0 py27_0
click 7.0 py27_0
cloudpickle 0.6.1 py27_0
configparser 3.5.0 py27_0
cryptography 1.8.1 py27_0
curl 7.52.1 0
cutadapt 1.12 py27_0 ipyrad
cython 0.29.2 py27he6710b0_0
cytoolz 0.9.0.1 py27h14c3975_1
dask 1.0.0 py27_0
dask-core 1.0.0 py27_0
decorator 4.3.0 py27_0
distributed 1.25.2 py27_0
docutils 0.14 py27_0
entrypoints 0.3 py27_0
enum34 1.1.6 py27_0
funcsigs 1.0.2 py27_0
functools32 3.2.3.2 py27_1
futures 3.2.0 py27_0
gmp 6.1.2 h6c8ec71_1
h5py 2.7.0 np113py27_0
hdf5 1.8.17 2
heapdict 1.0.0 py27_2
idna 2.6 py27_0
imagesize 1.1.0 py27_0
intel-openmp 2019.1 144
ipaddress 1.0.18 py27_0
ipykernel 4.10.0 py27_0
ipyparallel 6.2.3 py27_0
ipyrad 0.7.28 py27ha99686e_2 ipyrad
ipython 5.8.0 py27_0
ipython_genutils 0.2.0 py27_0
ipywidgets 7.4.2 py27_0
jinja2 2.10 py27_0
jsonschema 2.6.0 py27_0
jupyter 1.0.0 py27_7
jupyter_client 5.2.4 py27_0
jupyter_console 5.2.0 py27_1
jupyter_core 4.4.0 py27_0
libffi 3.2.1 1
libgcc 7.2.0 h69d50b8_2
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.3.0 hdf63c60_0
libsodium 1.0.16 h1bed415_0
libstdcxx-ng 8.2.0 hdf63c60_1
llvmlite 0.22.0 py27hdbca893_0
locket 0.2.0 py27_1
markupsafe 1.1.0 py27h7b6447c_0
mistune 0.8.4 py27h7b6447c_0
mkl 2019.1 144
mpi4py 2.0.0 py27_2
mpich2 1.4.1p1 0
msgpack-python 0.5.6 py27h6bb024c_1
nbconvert 5.3.1 py27_0
nbformat 4.4.0 py27_0
networkx 2.2 py27_1
notebook 5.7.4
And this conda env (a clean conda env in which I installed ipyrad 0.7.28) NOT WORKED:
alabaster 0.7.12 py27_0
asn1crypto 0.24.0 py27_0
babel 2.6.0 py27_0
backports 1.0 py27_1
backports.shutil_get_terminal_size 1.0.0 py27_2
backports_abc 0.5 py27_0
blas 1.0 mkl
bleach 3.1.0 py27_0
bokeh 1.0.4 py27_0
ca-certificates 2018.12.5 0
certifi 2018.11.29 py27_0
cffi 1.11.5 py27he75722e_1
chardet 3.0.4 py27_1
click 7.0 py27_0
cloudpickle 0.6.1 py27_0
configparser 3.5.0 py27_0
cryptography 2.3.1 py27hc365091_0
curl 7.61.0 h84994c4_0
cutadapt 1.12 py27_0 ipyrad
cython 0.29.2 py27he6710b0_0
cytoolz 0.9.0.1 py27h14c3975_1
dask 1.0.0 py27_0
dask-core 1.0.0 py27_0
dbus 1.13.6 h746ee38_0
decorator 4.3.0 py27_0
distributed 1.25.2 py27_0
docutils 0.14 py27_0
entrypoints 0.3 py27_0
enum34 1.1.6 py27_1
expat 2.2.6 he6710b0_0
fontconfig 2.13.0 h9420a91_0
freetype 2.9.1 h8a8886c_1
funcsigs 1.0.2 py27_0
functools32 3.2.3.2 py27_1
futures 3.2.0 py27_0
glib 2.56.2 hd408876_0
gmp 6.1.2 h6c8ec71_1
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.9.0 py27h7918eee_0
hdf5 1.10.4 hb1b8bf9_0
heapdict 1.0.0 py27_2
icu 58.2 h9c2bf20_1
idna 2.8 py27_0
imagesize 1.1.0 py27_0
intel-openmp 2019.1 144
ipaddress 1.0.22 py27_0
ipykernel 4.10.0 py27_0
ipyparallel 6.2.3 py27_0
ipyrad 0.7.28 py27ha99686e_2 ipyrad
ipython 5.8.0 py27_0
ipython_genutils 0.2.0 py27_0
ipywidgets 7.4.2 py27_0
jinja2 2.10 py27_0
jpeg 9b h024ee3a_2
jsonschema 2.6.0 py27_0
jupyter 1.0.0 py27_7
jupyter_client 5.2.4 py27_0
jupyter_console 5.2.0 py27_1
jupyter_core 4.4.0 py27_0
libcurl 7.61.0 h1ad7b7a_0
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.3.0 hdf63c60_0
libpng
jhoepke
@jhoepke
Jan 24 14:22
@isaacovercast As you can see this effects some installed package versions and I think the problem in step 7 stems from this (especially since installing ipyrad version 0.7.29 did not helped).
Jamie Hudson
@Jamie_Bio_twitter
Jan 24 16:00

Hi @isaacovercast , I'm getting the same "Invalid chromosome dictionary indexwat: 0" error as @tim-oconnor. My dataset is pairgbs, and I was previously also getting the "error in filter_stacks on chunk 0: ValueError(zero-size array to reduction operation minimum which has no identity)" error message at Step 7 during the 'filtering loci' step when my datatype in the params file was pairgbs. Changing this to "gbs" allowed me to also get down to the 'building vcf file' step where I receive the following error in the log file:


ipyrad [v.0.7.29]

Interactive assembly and analysis of RAD-seq data

Begin run: 2019-01-24 15:20
Using args {'force': True, 'threads': 16, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': None, 'cores': 16, 'params': '/scratch/jh25g11/Steve_ciona/params-steve_ciona_1.txt', 'branch': None, 'steps': '7', 'debug': False, 'new': None, 'download': None, 'MPI': False}
Platform info: ('Linux', 'green0617', '2.6.32-754.el6.x86_64', '#1 SMP Thu May 24 18:18:25 EDT 2018', 'x86_64')2019-01-24 15:24:36,113 pid=527 [write_outfiles.py] ERROR Invalid chromosome dictionary indexwat: 0
2019-01-24 15:24:36,247 pid=502 [write_outfiles.py] ERROR Invalid chromosome dictionary indexwat: 0
2019-01-24 15:24:36,688 pid=32720 [assembly.py] ERROR KeyError(0)
2019-01-24 15:24:36,858 pid=373 [write_outfiles.py] ERROR Invalid chromosome dictionary indexwat: 0
2019-01-24 15:24:37,317 pid=448 [write_outfiles.py] ERROR Invalid chromosome dictionary indexwat: 0
2019-01-24 15:24:37,444 pid=461 [write_outfiles.py] ERROR Invalid chromosome dictionary indexwat: 0
2019-01-24 15:24:37,728 pid=351 [write_outfiles.py] ERROR Invalid chromosome dictionary indexwat: 0

Updating to v.0.7.29 also did not resolve the error. @tim-oconnor were you able to get any further with your issue?

tommydevitt
@tommydevitt
Jan 24 19:00
@isaacovercast I've switched to a different HPC and am able to run everything fine now, so please ignore my last post.
tim-oconnor
@tim-oconnor
Jan 24 19:03
Hey @Jamie_Bio_twitter -- I think Isaac is on the case, but I haven't been able to get around the issue myself. I figure he has a backlog of issues to deal with so I'm hanging tight for the time being. I tried going back to v.0.7.18 (I think) in case it was a recent bug, but that didn't help anything.