installation error qiime2-2019.7:Segmentation fault

Technical Support
1

Hello，
everyone！ I want to install qiime2-2019.7 in a new linux device. I have installed miniconda3 and then I use this command “conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml” to install qiime2. It ran slowly, but then I met a error:

CondaHTTPError: HTTP 000 CONNECTION FAILED for url Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-fragment-insertion-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-sample-classifier-2019.7.1-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

(‘Connection broken: OSError("(104, ‘ECONNRESET’)")’, OSError("(104, ‘ECONNRESET’)"))
CondaError: Downloaded bytes did not match Content-Length
url: https://conda.anaconda.org/conda-forge/linux-64/pandas-0.24.2-py36hb3f55d8_0.tar.bz2
target_path: /root/miniconda3/pkgs/pandas-0.24.2-py36hb3f55d8_0.tar.bz2
Content-Length: 11667737
downloaded bytes: 11238147

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-9.1.0-hdf63c60_0.conda
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-dada2-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

(‘Connection broken: OSError("(104, ‘ECONNRESET’)")’, OSError("(104, ‘ECONNRESET’)"))
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/linux-64/bioconductor-dada2-1.10.0-r351hf484d3e_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-longitudinal-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-feature-table-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.3.0-hdf63c60_1.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-taxa-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-deblur-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2-vsearch-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2019.7/linux-64/q2templates-2019.7.0-py36_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

(base) root@iZ8vb3dk693jofeycgcci2Z:~# conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml
Collecting package metadata (repodata.json): failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/linux-64/repodata.json
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
ConnectionError(ReadTimeoutError(“HTTPSConnectionPool(host=‘conda.anaconda.org’, port=443): Read timed out.”))

Then I tried again! But another error appears:

(base) root@iZ8vb3dk693jofeycgcci2Z:~# conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml Collecting package metadata (repodata.json): done Solving environment: done Segmentation fault (base) root@iZ8vb3dk693jofeycgcci2Z:~# conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml Collecting package metadata (repodata.json): done Solving environment: done Segmentation fault
I really don't know how to solve it. Can anyone help me? Thankyou very much!
2

Hi @Zhanzhan!
What a mess, huh!? I haven't seen this issue before, but based on these errors:

I'm wondering whether you have an internet connectivity issue that is preventing Conda from downloading/installing the software correctly. Here are some things that might help you/others with troubleshooting the problem:

  • What version of linux is this? What version of MiniConda?
  • Have you had any other problems with the reliability of your internet connection?
  • If this is a portable machine, have you tried the same process using a different internet connection?
  • Do you have adequate privileges on the machine to download/install software?
  • Is this machine protected by a firewall that could be interfering?
3

Hello @ChrisKeefe Thank you very much!

  1. The linux is ubuntu 18.04, the miniconda is miniconda3
  2. It is a 16g ram cloud server. I didn’t find my machine has some internet connection problems.
  3. I used to install qiime2-2019.7 in a 2g ram cloud server and I succeeded.
  4. Maybe I don’t have any privileges in this machine? It is new.
  5. I don’t think the server has some firewall.
    Thank you! Maybe I need to install it again?
4

@ChrisKeefe I tried it again. When the installation interrupted, I used the same command to continue the installation and the same error segmentation fault appeared.

5

Hello @ChrisKeefe I have already solved this error. Just try it again and again.:sweat_smile:

3 Likes
6

Woohoo! Glad to hear it worked out for you, @Zhanzhan!

1 Like