Importing the multiarray numpy extension module failed

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Yung-Chih Lai

unread,

Oct 10, 2019, 5:22:56 AM10/10/19

to deepTools

Hi,

Many thanks for the great tool you developed. I use a MacBookPro11,5 with macOS Sierra version 10.12.6. I can run deepTools 2.5.3 on my notebook before. However, it doesn't work now and show error messages below. I don't really understand these error messages. Could you help me to successfully rerun the deepTools on my notebook? Should I reinstall a deepTools? Many thanks.

Best,

Gary

(base) gary > pwd

/Users/gary/Documents/Project/20190531_WIHN/deeptools

(base) gary > ll

total 29080904

-rw-r----- 1 gary staff 3.5G Oct 10 14:47 Chuong804.bam

-rw-r----- 1 gary staff 2.3M Oct 10 13:52 Chuong804.bam.bai

-rw-r----- 1 gary staff 4.1G Oct 10 14:59 Chuong805.bam

-rw-r----- 1 gary staff 2.5M Oct 10 13:53 Chuong805.bam.bai

-rw-r----- 1 gary staff 3.4G Oct 10 14:56 Chuong806.bam

-rw-r----- 1 gary staff 2.4M Oct 10 13:54 Chuong806.bam.bai

-rw-r----- 1 gary staff 2.8G Oct 10 14:52 Chuong808.bam

-rw-r----- 1 gary staff 2.3M Oct 10 13:55 Chuong808.bam.bai

-rw-r--r-- 1 gary staff 34M Jun 6 17:02 DC1.bigwig

-rw-r--r-- 1 gary staff 35M Jun 6 17:23 DC2.bigwig

-rw-r--r-- 1 gary staff 31M Jun 6 17:44 DM1.bigwig

-rw-r--r-- 1 gary staff 32M Jun 6 21:26 DM2.bigwig

-rw-r--r--@ 1 gary staff 6.3K Oct 10 15:23 note.txt

-rw-r--r--@ 1 gary staff 749B Oct 10 15:25 note2.txt

(base) gary > bamCoverage --bam Chuong804.bam --outFileName Chuong804.bigwig --outFileFormat=bigwig --scaleFactor=1 --binSize=1 --extendReads=0 --numberOfProcessors=6 --normalizeUsingRPKM --verbose

Traceback (most recent call last):

File "/Users/gary/anaconda/bin/bamCoverage", line 4, in <module>

from deeptools.bamCoverage import main

File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/bamCoverage.py", line 7, in <module>

import numpy as np

File "/Users/gary/.local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module>

from . import core

File "/Users/gary/.local/lib/python2.7/site-packages/numpy/core/__init__.py", line 71, in <module>

raise ImportError(msg)

ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the multiarray numpy extension module failed. Most

likely you are trying to import a failed build of numpy.

Here is how to proceed:

- If you're working with a numpy git repository, try `git clean -xdf`

(removes all files not under version control) and rebuild numpy.

- If you are simply trying to use the numpy version that you have installed:

your installation is broken - please reinstall numpy.

- If you have already reinstalled and that did not fix the problem, then:

1. Check that you are using the Python you expect (you're using /Users/gary/anaconda/bin/python),

and that you have no directories in your PATH or PYTHONPATH that can

interfere with the Python and numpy versions you're trying to use.

2. If (1) looks fine, you can open a new issue at

https://github.com/numpy/numpy/issues. Please include details on:

- how you installed Python

- how you installed numpy

- your operating system

- whether or not you have multiple versions of Python installed

- if you built from source, your compiler versions and ideally a build log

Note: this error has many possible causes, so please don't comment on

an existing issue about this - open a new one instead.

Original error was: No module named _multiarray_umath

(base) gary > deepTools

usage: deepTools [-h] [--version]

deepTools is a suite of python tools particularly developed for the efficient analysis of

high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

Each tool should be called by its own name as in the following example:

$ bamCoverage -b reads.bam -o coverage.bw

If you find deepTools useful for your research please cite as:

Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert,

Andreas S. Richter, Steffen Heyne, Friederike Dündar,

and Thomas Manke. 2016. "deepTools2: A next Generation Web Server for Deep-Sequencing

Data Analysis." Nucleic Acids Research, April. doi:10.1093/nar/gkw257.

[ Tools for BAM and bigWig file processing ]

multiBamSummary compute read coverages over bam files. Output used for plotCorrelation or plotPCA

multiBigwigSummary extract scores from bigwig files. Output used for plotCorrelation or plotPCA

correctGCBias corrects GC bias from bam file. Don't use it with ChIP data

bamCoverage computes read coverage per bins or regions

bamCompare computes log2 ratio and other operations of read coverage of two samples per bins or regions

bigwigCompare computes log2 ratio and other operations from bigwig scores of two samples per bins or regions

computeMatrix prepares the data from bigwig scores for plotting with plotHeatmap or plotProfile

[ Tools for QC ]

plotCorrelation plots heatmaps or scatterplots of data correlation

plotPCA plots PCA

plotFingerprint plots the distribution of enriched regions

bamPEFragmentSize returns the read length and paired-end distance from a bam file

computeGCBias computes and plots the GC bias of a sample

plotCoverage plots a histogram of read coverage

[Heatmaps and summary plots]

plotHeatmap plots one or multiple heatmaps of user selected regions over different genomic scores

plotProfile plots the average profile of user selected regions over different genomic scores

plotEnrichment plots the read/fragment coverage of one or more sets of regions

[Miscellaneous]

computeMatrixOperations Modifies the output of computeMatrix in a variety of ways.

For more information visit: http://deeptools.readthedocs.org

optional arguments:

-h, --help show this help message and exit

--version show program's version number and exit

(base) gary > deepTools --version

deepTools 2.5.3

(base) gary >

Devon Ryan

unread,

Oct 10, 2019, 5:24:53 AM10/10/19

to Yung-Chih Lai, deepTools

Looks like numpy got messed up, please reinstall it.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

> --
> You received this message because you are subscribed to the Google Groups "deepTools" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to deeptools+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/CAB11ZD72yJM9Fa2GTrd%2BuW_4abYCv2mvs_W1enykAawk90NufA%40mail.gmail.com.

Yung-Chih Lai

unread,

Oct 10, 2019, 9:48:38 AM10/10/19

to deepTools

Hi Devon,

Many thanks. However, there is an error message below when I install deppTools using conda below. Could you help me again? Thanks a lot.

Best,

Gary

(base) gary > conda install -c bioconda deeptools

WARNING conda.base.context:use_only_tar_bz2(632): Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3. Update or remove conda-build to get smaller downloads and faster extractions.

Collecting package metadata (repodata.json): done

Solving environment: failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

- anaconda==2018.12=py37_0 -> importlib_metadata==0.6=py37_0

- anaconda==2018.12=py37_0 -> mkl-service==1.1.2=py37hfbe908c_5

- mkl-service

- pkgs/main/osx-64::importlib_metadata==0.6=py37_0

- pkgs/main/osx-64::path.py==11.5.0=py37_0 -> importlib_metadata[version='>=0.5']

(base) gary >

> To unsubscribe from this group and stop receiving emails from it, send an email to deep...@googlegroups.com.

Devon Ryan

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Oct 10, 2019, 9:49:59 AM10/10/19

to Yung-Chih Lai, deepTools

You need to use the conda-forge channel too: `conda create -n
deepTools -c conda-forge -c bioconda deeptools`

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

> To unsubscribe from this group and stop receiving emails from it, send an email to deeptools+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/0a4fe376-e72d-4ccb-b156-e92b9ea2667e%40googlegroups.com.

Yung-Chih Lai

unread,

Oct 10, 2019, 10:20:17 AM10/10/19

to deepTools

Hi Devon,

Thanks a lot. I try both (1) pip install deeptools and (2) conda create -n deepTools -c conda-forge -c bioconda deeptools.However, both of them show the same error message: Segmentation fault: 11 (the detail below). Could you help me again? Many thanks.

Best,

Gary

(base) gary > pip install deeptools

Collecting deeptools

Downloading https://files.pythonhosted.org/packages/82/8e/d9d4b66b2ce1bd48f1db43357c8eb019ae3e8bb1bb7a9e82667db981e1df/deepTools-3.3.1.tar.gz (188kB)

100% |████████████████████████████████| 194kB 443kB/s

Requirement already satisfied: numpy>=1.9.0 in /anaconda3/lib/python3.7/site-packages (from deeptools) (1.15.4)

Requirement already satisfied: scipy>=0.17.0 in /anaconda3/lib/python3.7/site-packages (from deeptools) (1.1.0)

Requirement already satisfied: matplotlib>=3.0.0 in /anaconda3/lib/python3.7/site-packages (from deeptools) (3.0.2)

Collecting pysam>=0.14.0 (from deeptools)

Downloading https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz (3.2MB)

100% |████████████████████████████████| 3.2MB 1.0MB/s

Requirement already satisfied: numpydoc>=0.5 in /anaconda3/lib/python3.7/site-packages (from deeptools) (0.8.0)

Collecting pyBigWig>=0.2.1 (from deeptools)

Downloading https://files.pythonhosted.org/packages/b0/e2/cf945d541a10bb9c675f986d5bf0b0268544721054d17cc6260cfcfb3685/pyBigWig-0.3.17.tar.gz (64kB)

100% |████████████████████████████████| 71kB 2.2MB/s

Collecting py2bit>=0.2.0 (from deeptools)

Downloading https://files.pythonhosted.org/packages/53/bb/547a927bed736ead3dc909e1e552d57c9034bb9493eff80544c0cf6e4828/py2bit-0.3.0.tar.gz

Collecting plotly>=2.0.0 (from deeptools)

Downloading https://files.pythonhosted.org/packages/70/19/8437e22c84083a6d5d8a3c80f4edc73c9dcbb89261d07e6bd13b48752bbd/plotly-4.1.1-py2.py3-none-any.whl (7.1MB)

100% |████████████████████████████████| 7.1MB 366kB/s

Collecting deeptoolsintervals>=0.1.8 (from deeptools)

Downloading https://files.pythonhosted.org/packages/ac/1f/d10d6ad23c86c62d90d867d0506881a392ec6ef06885b858eaab868dd356/deeptoolsintervals-0.1.9.tar.gz (41kB)

100% |████████████████████████████████| 51kB 15.8MB/s

Requirement already satisfied: cycler>=0.10 in /anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.0->deeptools) (0.10.0)

Requirement already satisfied: kiwisolver>=1.0.1 in /anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.0->deeptools) (1.0.1)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.0->deeptools) (2.3.0)

Requirement already satisfied: python-dateutil>=2.1 in /anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.0->deeptools) (2.7.5)

Requirement already satisfied: sphinx>=1.2.3 in /anaconda3/lib/python3.7/site-packages (from numpydoc>=0.5->deeptools) (1.8.2)

Requirement already satisfied: Jinja2>=2.3 in /anaconda3/lib/python3.7/site-packages (from numpydoc>=0.5->deeptools) (2.10)

Collecting retrying>=1.3.3 (from plotly>=2.0.0->deeptools)

Downloading https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz

Requirement already satisfied: six in /anaconda3/lib/python3.7/site-packages (from plotly>=2.0.0->deeptools) (1.12.0)

Requirement already satisfied: setuptools in /anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=3.0.0->deeptools) (40.6.3)

Requirement already satisfied: Pygments>=2.0 in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (2.3.1)

Requirement already satisfied: docutils>=0.11 in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (0.14)

Requirement already satisfied: snowballstemmer>=1.1 in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (1.2.1)

Requirement already satisfied: babel!=2.0,>=1.3 in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (2.6.0)

Requirement already satisfied: alabaster<0.8,>=0.7 in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (0.7.12)

Requirement already satisfied: imagesize in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (1.1.0)

Requirement already satisfied: requests>=2.0.0 in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (2.21.0)

Requirement already satisfied: packaging in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (18.0)

Requirement already satisfied: sphinxcontrib-websupport in /anaconda3/lib/python3.7/site-packages (from sphinx>=1.2.3->numpydoc>=0.5->deeptools) (1.1.0)

Requirement already satisfied: MarkupSafe>=0.23 in /anaconda3/lib/python3.7/site-packages (from Jinja2>=2.3->numpydoc>=0.5->deeptools) (1.1.0)

Requirement already satisfied: pytz>=0a in /anaconda3/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.2.3->numpydoc>=0.5->deeptools) (2018.7)

Requirement already satisfied: idna<2.9,>=2.5 in /anaconda3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.2.3->numpydoc>=0.5->deeptools) (2.8)

Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /anaconda3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.2.3->numpydoc>=0.5->deeptools) (3.0.4)

Requirement already satisfied: certifi>=2017.4.17 in /anaconda3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.2.3->numpydoc>=0.5->deeptools) (2018.11.29)

Requirement already satisfied: urllib3<1.25,>=1.21.1 in /anaconda3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.2.3->numpydoc>=0.5->deeptools) (1.24.1)

Building wheels for collected packages: deeptools, pysam, pyBigWig, py2bit, deeptoolsintervals, retrying

Running setup.py bdist_wheel for deeptools ... done

Stored in directory: /Users/gary/Library/Caches/pip/wheels/3b/53/3e/e7f6d14bf8a185162d4308a9a07c540affccdf8f662ee6dafb

Running setup.py bdist_wheel for pysam ... done

Stored in directory: /Users/gary/Library/Caches/pip/wheels/85/ab/84/86ca6dda37a6fc85687b67be7345b735cd82f6584bea56f327

Running setup.py bdist_wheel for pyBigWig ... done

Stored in directory: /Users/gary/Library/Caches/pip/wheels/fb/27/2d/ac3e2e2d17894877fd3c4595ebd6fbd25ad805bfeab333f19b

Running setup.py bdist_wheel for py2bit ... done

Stored in directory: /Users/gary/Library/Caches/pip/wheels/df/66/b6/33fb9b65b31121127f1da60ca27948ecf8d4c59b0967298de8

Running setup.py bdist_wheel for deeptoolsintervals ... done

Stored in directory: /Users/gary/Library/Caches/pip/wheels/f1/60/60/e513c6246f67379f6e1b8d09448cdf913bac3851f96bd42e94

Running setup.py bdist_wheel for retrying ... done

Stored in directory: /Users/gary/Library/Caches/pip/wheels/d7/a9/33/acc7b709e2a35caa7d4cae442f6fe6fbf2c43f80823d46460c

Successfully built deeptools pysam pyBigWig py2bit deeptoolsintervals retrying

Installing collected packages: pysam, pyBigWig, py2bit, retrying, plotly, deeptoolsintervals, deeptools

Successfully installed deeptools-3.3.1 deeptoolsintervals-0.1.9 plotly-4.1.1 py2bit-0.3.0 pyBigWig-0.3.17 pysam-0.15.3 retrying-1.3.3

(base) gary > pwd

/Users/gary/Documents/Project/20190531_WIHN/deeptools

(base) gary > ll

total 83266496

-rw-r----- 1 gary staff 3.1G Oct 10 19:06 Chuong803_R1.bam

-rw-r----- 1 gary staff 2.3M Oct 10 17:31 Chuong803_R1.bam.bai

-rw-r----- 1 gary staff 3.5G Oct 10 14:47 Chuong804.bam

-rw-r----- 1 gary staff 2.3M Oct 10 13:52 Chuong804.bam.bai

-rw-r----- 1 gary staff 4.1G Oct 10 14:59 Chuong805.bam

-rw-r----- 1 gary staff 2.5M Oct 10 13:53 Chuong805.bam.bai

-rw-r----- 1 gary staff 3.4G Oct 10 14:56 Chuong806.bam

-rw-r----- 1 gary staff 2.4M Oct 10 13:54 Chuong806.bam.bai

-rw-r----- 1 gary staff 6.2G Oct 10 19:57 Chuong807_R1.bam

-rw-r----- 1 gary staff 2.8M Oct 10 17:32 Chuong807_R1.bam.bai

-rw-r----- 1 gary staff 2.8G Oct 10 14:52 Chuong808.bam

-rw-r----- 1 gary staff 2.3M Oct 10 13:55 Chuong808.bam.bai

-rw-r----- 1 gary staff 6.7G Oct 10 20:10 Chuong810_R1.bam

-rw-r----- 1 gary staff 3.4M Oct 10 17:37 Chuong810_R1.bam.bai

-rw-r----- 1 gary staff 3.7G Oct 10 19:33 Chuong811_R1.bam

-rw-r----- 1 gary staff 2.5M Oct 10 17:38 Chuong811_R1.bam.bai

-rw-r----- 1 gary staff 1.8G Oct 10 18:45 Chuong812_R1.bam

-rw-r----- 1 gary staff 2.1M Oct 10 17:40 Chuong812_R1.bam.bai

-rw-r----- 1 gary staff 4.3G Oct 10 19:49 Chuong813_R1.bam

-rw-r----- 1 gary staff 3.3M Oct 10 17:42 Chuong813_R1.bam.bai

-rw-r--r-- 1 gary staff 34M Jun 6 17:02 DC1.bigwig

-rw-r--r-- 1 gary staff 35M Jun 6 17:23 DC2.bigwig

-rw-r--r-- 1 gary staff 31M Jun 6 17:44 DM1.bigwig

-rw-r--r-- 1 gary staff 32M Jun 6 21:26 DM2.bigwig

-rw-r--r--@ 1 gary staff 6.3K Oct 10 15:23 note.txt

-rw-r--r--@ 1 gary staff 749B Oct 10 17:16 note2.txt

(base) gary > bamCoverage --bam Chuong804.bam --outFileName Chuong804.bigwig --outFileFormat=bigwig --scaleFactor=1 --binSize=1 --extendReads=0 --numberOfProcessors=6 --normalizeUsingRPKM --verbose

Segmentation fault: 11

(base) gary > conda create -n deepTools -c conda-forge -c bioconda deeptools

Collecting package metadata (repodata.json): done

Solving environment: done

==> WARNING: A newer version of conda exists. <==

current version: 4.7.5

latest version: 4.7.12

Please update conda by running

$ conda update -n base conda

## Package Plan ##

environment location: /anaconda3/envs/deepTools

added / updated specs:

- deeptools

The following packages will be downloaded:

package | build

---------------------------|-----------------

bcftools-1.8 | h4da6232_3 775 KB bioconda

bzip2-1.0.8 | h01d97ff_1 148 KB conda-forge

ca-certificates-2019.9.11 | hecc5488_0 143 KB conda-forge

certifi-2019.6.16 | py36_1 149 KB conda-forge

curl-7.65.3 | h22ea746_0 125 KB conda-forge

cycler-0.10.0 | py_1 8 KB conda-forge

deeptools-3.3.1 | py_0 139 KB bioconda

deeptoolsintervals-0.1.9 | py36h01d97ff_0 72 KB bioconda

freetype-2.10.0 | h24853df_1 894 KB conda-forge

htslib-1.7 | 0 1.2 MB bioconda

kiwisolver-1.1.0 | py36h770b8ee_0 57 KB conda-forge

krb5-1.16.3 | hcfa6398_1001 1.1 MB conda-forge

libblas-3.8.0 | 13_openblas 10 KB conda-forge

libcblas-3.8.0 | 13_openblas 10 KB conda-forge

libcurl-7.65.3 | h16faf7d_0 547 KB conda-forge

libcxx-9.0.0 | 0 1002 KB conda-forge

libcxxabi-9.0.0 | 0 142 KB conda-forge

libdeflate-1.3 | h01d97ff_0 63 KB conda-forge

libedit-3.1.20170329 | hcfe32e1_1001 152 KB conda-forge

libffi-3.2.1 | h6de7cb9_1006 43 KB conda-forge

libgfortran-4.0.0 | 2 716 KB conda-forge

liblapack-3.8.0 | 13_openblas 10 KB conda-forge

libopenblas-0.3.7 | h4bb4525_1 8.3 MB conda-forge

libpng-1.6.37 | h2573ce8_0 298 KB conda-forge

libssh2-1.8.2 | hcdc9a53_2 221 KB conda-forge

llvm-openmp-9.0.0 | h40edb58_0 266 KB conda-forge

matplotlib-3.1.1 | py36_1 6 KB conda-forge

matplotlib-base-3.1.1 | py36h3a684a6_1 6.6 MB conda-forge

ncurses-6.1 | h0a44026_1002 1.3 MB conda-forge

numpy-1.17.2 | py36h6b0580a_0 5.0 MB conda-forge

openssl-1.1.1c | h01d97ff_0 1.9 MB conda-forge

pip-19.2.3 | py36_0 1.9 MB conda-forge

plotly-4.1.1 | py_0 4.0 MB conda-forge

py2bit-0.3.0 | py36h1de35cc_2 20 KB bioconda

pybigwig-0.3.17 | py36haec6b85_0 68 KB bioconda

pyparsing-2.4.2 | py_0 57 KB conda-forge

pysam-0.14.1 | py36hae42fb6_1 2.0 MB bioconda

python-3.6.7 | h94afb7f_1005 20.6 MB conda-forge

python-dateutil-2.8.0 | py_0 219 KB conda-forge

readline-8.0 | hcfe32e1_0 415 KB conda-forge

retrying-1.3.3 | py_2 11 KB conda-forge

samtools-1.7 | 1 513 KB bioconda

scipy-1.3.1 | py36h7e0e109_2 18.3 MB conda-forge

setuptools-41.4.0 | py36_0 621 KB conda-forge

six-1.12.0 | py36_1000 22 KB conda-forge

sqlite-3.30.0 | h93121df_0 2.5 MB conda-forge

tk-8.6.9 | h2573ce8_1003 3.2 MB conda-forge

tornado-6.0.3 | py36h01d97ff_0 636 KB conda-forge

wheel-0.33.6 | py36_0 35 KB conda-forge

xz-5.2.4 | h1de35cc_1001 268 KB conda-forge

zlib-1.2.11 | h01d97ff_1006 101 KB conda-forge

------------------------------------------------------------

Total: 86.5 MB

The following NEW packages will be INSTALLED:

bcftools bioconda/osx-64::bcftools-1.8-h4da6232_3

bzip2 conda-forge/osx-64::bzip2-1.0.8-h01d97ff_1

ca-certificates conda-forge/osx-64::ca-certificates-2019.9.11-hecc5488_0

certifi conda-forge/osx-64::certifi-2019.6.16-py36_1

curl conda-forge/osx-64::curl-7.65.3-h22ea746_0

cycler conda-forge/noarch::cycler-0.10.0-py_1

deeptools bioconda/noarch::deeptools-3.3.1-py_0

deeptoolsintervals bioconda/osx-64::deeptoolsintervals-0.1.9-py36h01d97ff_0

freetype conda-forge/osx-64::freetype-2.10.0-h24853df_1

htslib bioconda/osx-64::htslib-1.7-0

kiwisolver conda-forge/osx-64::kiwisolver-1.1.0-py36h770b8ee_0

krb5 conda-forge/osx-64::krb5-1.16.3-hcfa6398_1001

libblas conda-forge/osx-64::libblas-3.8.0-13_openblas

libcblas conda-forge/osx-64::libcblas-3.8.0-13_openblas

libcurl conda-forge/osx-64::libcurl-7.65.3-h16faf7d_0

libcxx conda-forge/osx-64::libcxx-9.0.0-0

libcxxabi conda-forge/osx-64::libcxxabi-9.0.0-0

libdeflate conda-forge/osx-64::libdeflate-1.3-h01d97ff_0

libedit conda-forge/osx-64::libedit-3.1.20170329-hcfe32e1_1001

libffi conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006

libgfortran conda-forge/osx-64::libgfortran-4.0.0-2

liblapack conda-forge/osx-64::liblapack-3.8.0-13_openblas

libopenblas conda-forge/osx-64::libopenblas-0.3.7-h4bb4525_1

libpng conda-forge/osx-64::libpng-1.6.37-h2573ce8_0

libssh2 conda-forge/osx-64::libssh2-1.8.2-hcdc9a53_2

llvm-openmp conda-forge/osx-64::llvm-openmp-9.0.0-h40edb58_0

matplotlib conda-forge/osx-64::matplotlib-3.1.1-py36_1

matplotlib-base conda-forge/osx-64::matplotlib-base-3.1.1-py36h3a684a6_1

ncurses conda-forge/osx-64::ncurses-6.1-h0a44026_1002

numpy conda-forge/osx-64::numpy-1.17.2-py36h6b0580a_0

openssl conda-forge/osx-64::openssl-1.1.1c-h01d97ff_0

pip conda-forge/osx-64::pip-19.2.3-py36_0

plotly conda-forge/noarch::plotly-4.1.1-py_0

py2bit bioconda/osx-64::py2bit-0.3.0-py36h1de35cc_2

pybigwig bioconda/osx-64::pybigwig-0.3.17-py36haec6b85_0

pyparsing conda-forge/noarch::pyparsing-2.4.2-py_0

pysam bioconda/osx-64::pysam-0.14.1-py36hae42fb6_1

python conda-forge/osx-64::python-3.6.7-h94afb7f_1005

python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0

readline conda-forge/osx-64::readline-8.0-hcfe32e1_0

retrying conda-forge/noarch::retrying-1.3.3-py_2

samtools bioconda/osx-64::samtools-1.7-1

scipy conda-forge/osx-64::scipy-1.3.1-py36h7e0e109_2

setuptools conda-forge/osx-64::setuptools-41.4.0-py36_0

six conda-forge/osx-64::six-1.12.0-py36_1000

sqlite conda-forge/osx-64::sqlite-3.30.0-h93121df_0

tk conda-forge/osx-64::tk-8.6.9-h2573ce8_1003

tornado conda-forge/osx-64::tornado-6.0.3-py36h01d97ff_0

wheel conda-forge/osx-64::wheel-0.33.6-py36_0

xz conda-forge/osx-64::xz-5.2.4-h1de35cc_1001

zlib conda-forge/osx-64::zlib-1.2.11-h01d97ff_1006

Proceed ([y]/n)? y

Downloading and Extracting Packages

libcblas-3.8.0 | 10 KB | ##################################################################################################################################### | 100%

bcftools-1.8 | 775 KB | ##################################################################################################################################### | 100%

plotly-4.1.1 | 4.0 MB | ##################################################################################################################################### | 100%

cycler-0.10.0 | 8 KB | ##################################################################################################################################### | 100%

xz-5.2.4 | 268 KB | ##################################################################################################################################### | 100%

readline-8.0 | 415 KB | ##################################################################################################################################### | 100%

krb5-1.16.3 | 1.1 MB | ##################################################################################################################################### | 100%

libcxx-9.0.0 | 1002 KB | ##################################################################################################################################### | 100%

libssh2-1.8.2 | 221 KB | ##################################################################################################################################### | 100%

py2bit-0.3.0 | 20 KB | ##################################################################################################################################### | 100%

libblas-3.8.0 | 10 KB | ##################################################################################################################################### | 100%

openssl-1.1.1c | 1.9 MB | ##################################################################################################################################### | 100%

libcurl-7.65.3 | 547 KB | ##################################################################################################################################### | 100%

python-3.6.7 | 20.6 MB | ##################################################################################################################################### | 100%

matplotlib-base-3.1. | 6.6 MB | ##################################################################################################################################### | 100%

libdeflate-1.3 | 63 KB | ##################################################################################################################################### | 100%

htslib-1.7 | 1.2 MB | ##################################################################################################################################### | 100%

pysam-0.14.1 | 2.0 MB | ##################################################################################################################################### | 100%

libffi-3.2.1 | 43 KB | ##################################################################################################################################### | 100%

wheel-0.33.6 | 35 KB | ##################################################################################################################################### | 100%

deeptools-3.3.1 | 139 KB | ##################################################################################################################################### | 100%

samtools-1.7 | 513 KB | ##################################################################################################################################### | 100%

bzip2-1.0.8 | 148 KB | ##################################################################################################################################### | 100%

pybigwig-0.3.17 | 68 KB | ##################################################################################################################################### | 100%

matplotlib-3.1.1 | 6 KB | ##################################################################################################################################### | 100%

pip-19.2.3 | 1.9 MB | ##################################################################################################################################### | 100%

pyparsing-2.4.2 | 57 KB | ##################################################################################################################################### | 100%

libopenblas-0.3.7 | 8.3 MB | ##################################################################################################################################### | 100%

libcxxabi-9.0.0 | 142 KB | ##################################################################################################################################### | 100%

numpy-1.17.2 | 5.0 MB | ##################################################################################################################################### | 100%

libedit-3.1.20170329 | 152 KB | ##################################################################################################################################### | 100%

liblapack-3.8.0 | 10 KB | ##################################################################################################################################### | 100%

python-dateutil-2.8. | 219 KB | ##################################################################################################################################### | 100%

ncurses-6.1 | 1.3 MB | ##################################################################################################################################### | 100%

zlib-1.2.11 | 101 KB | ##################################################################################################################################### | 100%

tk-8.6.9 | 3.2 MB | ##################################################################################################################################### | 100%

libpng-1.6.37 | 298 KB | ##################################################################################################################################### | 100%

certifi-2019.6.16 | 149 KB | ##################################################################################################################################### | 100%

curl-7.65.3 | 125 KB | ##################################################################################################################################### | 100%

deeptoolsintervals-0 | 72 KB | ##################################################################################################################################### | 100%

llvm-openmp-9.0.0 | 266 KB | ##################################################################################################################################### | 100%

ca-certificates-2019 | 143 KB | ##################################################################################################################################### | 100%

setuptools-41.4.0 | 621 KB | ##################################################################################################################################### | 100%

six-1.12.0 | 22 KB | ##################################################################################################################################### | 100%

scipy-1.3.1 | 18.3 MB | ##################################################################################################################################### | 100%

retrying-1.3.3 | 11 KB | ##################################################################################################################################### | 100%

freetype-2.10.0 | 894 KB | ##################################################################################################################################### | 100%

sqlite-3.30.0 | 2.5 MB | ##################################################################################################################################### | 100%

tornado-6.0.3 | 636 KB | ##################################################################################################################################### | 100%

libgfortran-4.0.0 | 716 KB | ##################################################################################################################################### | 100%

kiwisolver-1.1.0 | 57 KB | ##################################################################################################################################### | 100%

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

# To activate this environment, use

# $ conda activate deepTools

# To deactivate an active environment, use

# $ conda deactivate

(base) gary > pwd

/Users/gary/Documents/Project/20190531_WIHN/deeptools

(base) gary > ll

total 83266496

-rw-r----- 1 gary staff 3.1G Oct 10 19:06 Chuong803_R1.bam

-rw-r----- 1 gary staff 2.3M Oct 10 17:31 Chuong803_R1.bam.bai

-rw-r----- 1 gary staff 3.5G Oct 10 14:47 Chuong804.bam

-rw-r----- 1 gary staff 2.3M Oct 10 13:52 Chuong804.bam.bai

-rw-r----- 1 gary staff 4.1G Oct 10 14:59 Chuong805.bam

-rw-r----- 1 gary staff 2.5M Oct 10 13:53 Chuong805.bam.bai

-rw-r----- 1 gary staff 3.4G Oct 10 14:56 Chuong806.bam

-rw-r----- 1 gary staff 2.4M Oct 10 13:54 Chuong806.bam.bai

-rw-r----- 1 gary staff 6.2G Oct 10 19:57 Chuong807_R1.bam

-rw-r----- 1 gary staff 2.8M Oct 10 17:32 Chuong807_R1.bam.bai

-rw-r----- 1 gary staff 2.8G Oct 10 14:52 Chuong808.bam

-rw-r----- 1 gary staff 2.3M Oct 10 13:55 Chuong808.bam.bai

-rw-r----- 1 gary staff 6.7G Oct 10 20:10 Chuong810_R1.bam

-rw-r----- 1 gary staff 3.4M Oct 10 17:37 Chuong810_R1.bam.bai

-rw-r----- 1 gary staff 3.7G Oct 10 19:33 Chuong811_R1.bam

-rw-r----- 1 gary staff 2.5M Oct 10 17:38 Chuong811_R1.bam.bai

-rw-r----- 1 gary staff 1.8G Oct 10 18:45 Chuong812_R1.bam

-rw-r----- 1 gary staff 2.1M Oct 10 17:40 Chuong812_R1.bam.bai

-rw-r----- 1 gary staff 4.3G Oct 10 19:49 Chuong813_R1.bam

-rw-r----- 1 gary staff 3.3M Oct 10 17:42 Chuong813_R1.bam.bai

-rw-r--r-- 1 gary staff 34M Jun 6 17:02 DC1.bigwig

-rw-r--r-- 1 gary staff 35M Jun 6 17:23 DC2.bigwig

-rw-r--r-- 1 gary staff 31M Jun 6 17:44 DM1.bigwig

-rw-r--r-- 1 gary staff 32M Jun 6 21:26 DM2.bigwig

-rw-r--r--@ 1 gary staff 6.3K Oct 10 15:23 note.txt

-rw-r--r--@ 1 gary staff 749B Oct 10 17:16 note2.txt

(base) gary > bamCoverage --bam Chuong804.bam --outFileName Chuong804.bigwig --outFileFormat=bigwig --scaleFactor=1 --binSize=1 --extendReads=0 --numberOfProcessors=6 --normalizeUsingRPKM --verbose

Segmentation fault: 11

(base) gary >

Yung-Chih Lai

unread,

Oct 10, 2019, 11:11:33 AM10/10/19

to deepTools

Hi Devon,

I try to uninstall deepTools using pip and install deepTools again using conda (the detail below). However, it still doesn't work. Could you help me again? Thanks a lot.

Best,

Gary

(base) gary > pip uninstall deepTools

Uninstalling deepTools-3.3.1:

Would remove:

/anaconda3/bin/alignmentSieve

/anaconda3/bin/bamCompare

/anaconda3/bin/bamCoverage

/anaconda3/bin/bamPEFragmentSize

/anaconda3/bin/bigwigCompare

/anaconda3/bin/computeGCBias

/anaconda3/bin/computeMatrix

/anaconda3/bin/computeMatrixOperations

/anaconda3/bin/correctGCBias

/anaconda3/bin/deeptools

/anaconda3/bin/estimateReadFiltering

/anaconda3/bin/estimateScaleFactor

/anaconda3/bin/multiBamSummary

/anaconda3/bin/multiBigwigSummary

/anaconda3/bin/plotCorrelation

/anaconda3/bin/plotCoverage

/anaconda3/bin/plotEnrichment

/anaconda3/bin/plotFingerprint

/anaconda3/bin/plotHeatmap

/anaconda3/bin/plotPCA

/anaconda3/bin/plotProfile

/anaconda3/lib/python3.7/site-packages/deepTools-3.3.1.dist-info/*

/anaconda3/lib/python3.7/site-packages/deeptools/*

Proceed (y/n)? y

Successfully uninstalled deepTools-3.3.1

(base) gary > conda create -n deepTools -c conda-forge -c bioconda deeptools

WARNING: A conda environment already exists at '/anaconda3/envs/deepTools'

Remove existing environment (y/[n])? y

Collecting package metadata (repodata.json): done

Solving environment: done

==> WARNING: A newer version of conda exists. <==

current version: 4.7.5

latest version: 4.7.12

Please update conda by running

$ conda update -n base conda

## Package Plan ##

environment location: /anaconda3/envs/deepTools

added / updated specs:

- deeptools

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

# To activate this environment, use

# $ conda activate deepTools

# To deactivate an active environment, use

# $ conda deactivate

(base) gary > bamCoverage --bam Chuong804.bam --outFileName Chuong804.bigwig --outFileFormat=bigwig --scaleFactor=1 --binSize=1 --extendReads=0 --numberOfProcessors=6 --normalizeUsingRPKM --verbose

Traceback (most recent call last):

Devon Ryan

unread,

Oct 10, 2019, 3:34:29 PM10/10/19

to Yung-Chih Lai, deepTools

Sorry, I don't know why your python installation is broken.

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/aa48beb4-d71b-4f2e-9fab-97ece4837c06%40googlegroups.com.

Yung-Chih Lai

unread,

Oct 11, 2019, 4:57:15 AM10/11/19

to Devon Ryan, deepTools

Dear Devon,

The deepTools is a vital bioinformatics tool to analyze our RNAseq, ChIPseq, and ATACseq data. I can't afford to lose it. I believe the issue is caused by several versions of python in my MacBook Pro when I install different bioinformatics tools (the detail below). Could you help me to fix my corrupted python installation? Please let me know if you need any more information. Thank you so much.

Best regards

Gary

(base) gary > which -a python
/anaconda3/bin/python
/Users/gary/anaconda/bin/python
/usr/bin/python
(base) gary > python
Python 3.7.1 (default, Dec 14 2018, 13:28:58)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()

(base) gary > cd /anaconda3/bin/
(base) gary > pwd
/anaconda3/bin
(base) gary > ll | grep python
-rwxrwxr-x 1 gary wheel 233B Mar 4 2019 ipython
-rwxrwxr-x 1 gary wheel 233B Mar 4 2019 ipython3
lrwxr-xr-x 1 gary wheel 9B Mar 4 2019 python -> python3.7
-rwxrwxr-x 1 gary wheel 107B Mar 4 2019 python.app
lrwxr-xr-x 1 gary wheel 9B Mar 4 2019 python3 -> python3.7
lrwxr-xr-x 1 gary wheel 17B Mar 4 2019 python3-config -> python3.7m-config
-rwxrwxr-x 1 gary wheel 4.0M Mar 4 2019 python3.7
lrwxr-xr-x 1 gary wheel 17B Mar 4 2019 python3.7-config -> python3.7m-config
lrwxr-xr-x 1 gary wheel 9B Mar 4 2019 python3.7m -> python3.7
-rwxrwxr-x 1 gary wheel 2.0K Mar 4 2019 python3.7m-config
-rwxrwxr-x 1 gary wheel 107B Mar 4 2019 pythonw

(base) gary > cd /Users/gary/anaconda/bin
(base) gary > pwd
/Users/gary/anaconda/bin
(base) gary > ll | grep python
-rwxrwxr-x 1 gary staff 250B Nov 29 2015 activate-global-python-argcomplete
-rwxrwxr-x 1 gary staff 159B Nov 29 2015 ipython
-rwxrwxr-x 1 gary staff 159B Nov 29 2015 ipython2
-rwxrwxr-x 2 gary staff 41B Aug 29 2015 ipython_mac.command
lrwxr-xr-x 1 gary staff 9B Mar 23 2017 python -> python2.7
-rwxrwxr-x 1 gary staff 270B Nov 29 2015 python-argcomplete-check-easy-install-script
lrwxr-xr-x 1 gary staff 16B Mar 23 2017 python-config -> python2.7-config
-rwxrwxr-x 1 gary staff 127B Nov 29 2015 python.app
lrwxr-xr-x 1 gary staff 9B Mar 23 2017 python2 -> python2.7
lrwxr-xr-x 1 gary staff 16B Mar 23 2017 python2-config -> python2.7-config
-rwxrwxr-x 1 gary staff 8.9K Dec 21 2016 python2.7
-rwxrwxr-x 1 gary staff 1.7K Mar 23 2017 python2.7-config
-rwxrwxr-x 1 gary staff 127B Nov 29 2015 pythonw
-rwxrwxr-x 1 gary staff 236B Nov 29 2015 register-python-argcomplete

(base) gary > cd /usr/bin
(base) gary > pwd
/usr/bin
(base) gary > ll | grep python
-rwxr-xr-x 1 root wheel 65K Jul 15 2017 python
-rwxr-xr-x 5 root wheel 925B Feb 7 2017 python-config
lrwxr-xr-x 1 root wheel 75B Sep 8 2017 python2.6 -> ../../System/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6
lrwxr-xr-x 1 root wheel 82B Sep 8 2017 python2.6-config -> ../../System/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6-config
lrwxr-xr-x 1 root wheel 75B Sep 8 2017 python2.7 -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
lrwxr-xr-x 1 root wheel 82B Sep 8 2017 python2.7-config -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config
-rwxr-xr-x 1 root wheel 65K Jul 15 2017 pythonw
lrwxr-xr-x 1 root wheel 76B Sep 8 2017 pythonw2.6 -> ../../System/Library/Frameworks/Python.framework/Versions/2.6/bin/pythonw2.6
lrwxr-xr-x 1 root wheel 76B Sep 8 2017 pythonw2.7 -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/pythonw2.7

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