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Process get_software_versions terminated with an error exit status (1) #102

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weinformatics opened this issue Sep 16, 2019 · 20 comments
Closed

Process get_software_versions terminated with an error exit status (1) #102

weinformatics opened this issue Sep 16, 2019 · 20 comments

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@weinformatics
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Hi, I met this issue as follows.

clldebian10@clldebian10:~$ ./nextflow run nf-core/ampliseq -r 1.1.0 -profile docker --reads '/mnt/weinfo/users/cailiangliang/data/16srna20190531/' \
> --FW_primer GTGCCAGCMGCCGCGGTAA --RV_primer GGACTACHVGGGTWTCTAAT \
> --classifier "/mnt/weinfo/users/cailiangliang/data/16srna20190531/classifier.qza" \
> --retain_untrimmed \
> --trunclenf 250 --trunclenr 250 \
> --metadata "/mnt/weinfo/users/cailiangliang/data/16srna20190531/Metadatasec.tsv" \
> --max_cpus 4 \
> --max_memory '40.GB'
N E X T F L O W  ~  version 19.07.0
Launching `nf-core/ampliseq` [pedantic_banach] - revision: 57e1ee2f90 [1.1.0]
[2m----------------------------------------------------
	                                ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
	                                `._,._,'
  nf-core/ampliseq v1.1.0
----------------------------------------------------
Pipeline Name     : nf-core/ampliseq
Pipeline Release  : 1.1.0
Run Name          : pedantic_banach
Reads             : /mnt/weinfo/users/cailiangliang/data/16srna20190531/
Data Type         : Paired-End
Max Resources     : 40.GB memory, 4 cpus, 10d time per job
Container         : docker - nfcore/ampliseq:1.1.0
Output dir        : ./results
Launch dir        : /home/clldebian10
Working dir       : /home/clldebian10/work
Script dir        : /home/clldebian10/.nextflow/assets/nf-core/ampliseq
User              : clldebian10
Config Profile    : docker
[2m----------------------------------------------------
executor >  local (7)
[41/474512] process > get_software_versions          [  0%] 0 of 1
[b3/5492f7] process > fastqc (lstdfjL10_S006_L001)   [ 50%] 2 of 4, failed: 2
[74/0b15f9] process > trimming (lstdf2L08_S004_L001) [  0%] 0 of 2
[-        ] process > multiqc                        -
[-        ] process > qiime_import                   -
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
executor >  local (7)
[41/474512] process > get_software_versions          [100%] 1 of 1, failed: 1 ✘
[b3/5492f7] process > fastqc (lstdfjL10_S006_L001)   [ 50%] 2 of 4, failed: 2
[b3/4d2652] process > trimming (lstdf1L04_S001_L001) [ 50%] 1 of 2, failed: 1
[-        ] process > multiqc                        -
[-        ] process > qiime_import                   -
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
executor >  local (7)
[41/474512] process > get_software_versions          [100%] 1 of 1, failed: 1 ✘
[de/4cdf7b] process > fastqc (lstdf2L08_S004_L001)   [ 75%] 3 of 4, failed: 3
[b3/4d2652] process > trimming (lstdf1L04_S001_L001) [ 50%] 1 of 2, failed: 1
[-        ] process > multiqc                        -
[-        ] process > qiime_import                   -
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
executor >  local (7)
[41/474512] process > get_software_versions          [100%] 1 of 1, failed: 1 ✘
[b3/5492f7] process > fastqc (lstdfjL10_S006_L001)   [100%] 4 of 4, failed: 4
[74/0b15f9] process > trimming (lstdf2L08_S004_L001) [100%] 2 of 2, failed: 2
[-        ] process > multiqc                        -
[-        ] process > qiime_import                   -
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
executor >  local (7)
[41/474512] process > get_software_versions          [100%] 1 of 1, failed: 1 ✘
[b3/5492f7] process > fastqc (lstdfjL10_S006_L001)   [100%] 4 of 4, failed: 4
[74/0b15f9] process > trimming (lstdf2L08_S004_L001) [100%] 2 of 2, failed: 2
[-        ] process > multiqc                        -
[-        ] process > qiime_import                   -
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
executor >  local (7)
[41/474512] process > get_software_versions          [100%] 1 of 1, failed: 1 ✘
[b3/5492f7] process > fastqc (lstdfjL10_S006_L001)   [100%] 4 of 4, failed: 4
[74/0b15f9] process > trimming (lstdf2L08_S004_L001) [100%] 2 of 2, failed: 2
[-        ] process > multiqc                        -
[-        ] process > qiime_import                   -
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[-        ] process > metadata_category_all          -
[-        ] process > metadata_category_pairwise     -
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[-        ] process > output_documentation           -
Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
[ee/7c3a46] NOTE: Process `fastqc (lstdf2L03_S003_L001)` terminated with an error exit status (1) -- Error is ignored
[e4/20239d] NOTE: Process `fastqc (lstdf1L09_S002_L001)` terminated with an error exit status (1) -- Error is ignored
[de/4cdf7b] NOTE: Process `fastqc (lstdf2L08_S004_L001)` terminated with an error exit status (1) -- Error is ignored
[b3/5492f7] NOTE: Process `fastqc (lstdfjL10_S006_L001)` terminated with an error exit status (1) -- Error is ignored
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (1)

Command executed:

  echo 1.1.0 > v_pipeline.txt
  echo 19.07.0 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  cutadapt --version > v_cutadapt.txt
  qiime --version > v_qiime.txt
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.run: line 186: uname: command not found
  .command.run: line 138: grep: command not found
  .command.run: line 139: grep: command not found
  .command.run: line 200: date: command not found
  Command 'ps' required by nextflow to collect task metrics cannot be found

Work dir:
  /home/clldebian10/work/41/474512f051ca5d5f4ffc1ae162a47e

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
@d4straub
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Collaborator

Hi there,
the pipeline seems to have no access to any program. Are you sure you have installed docker correctly? In #55 this was already discussed, does that help?

@weinformatics
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Author

weinformatics commented Sep 16, 2019 •
edited
Loading

Hi there,
the pipeline seems to have no access to any program. Are you sure you have installed docker correctly? In #55 this was already discussed, does that help?

I install my Docker refer to official instruction: And run the test.

clldebian9@clldebian9:~$ docker -v
Docker version 18.06.3-ce, build d7080c1
clldebian9@clldebian9:~$ docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
nfcore/ampliseq     1.1.0               8127552fd3c2        2 months ago        6.27GB
hello-world         latest              fce289e99eb9        8 months ago        1.84kB
nfcore/ampliseq     1.0.0               a09058c4d517        9 months ago        6.29GB
clldebian9@clldebian9:~$ docker run hello-world

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

clldebian9@clldebian9:~$

My java and nextflow verison

clldebian9@clldebian9:~$ java -version
openjdk version "1.8.0_222"
OpenJDK Runtime Environment (build 1.8.0_222-8u222-b10-1~deb9u1-b10)
OpenJDK 64-Bit Server VM (build 25.222-b10, mixed mode)
clldebian9@clldebian9:~$ ./nextflow -v
nextflow version 19.07.0.5106

@d4straub
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Collaborator

Hm, looks like docker isn't the problem. Maybe @apeltzer has another idea?

@weinformatics
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Author

thanks. @d4straub can you tell me your nfcore run environment including OS name and version, jdk version, docker version and nextflow version ? I can try again.

@d4straub
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Collaborator

Not sure if it helps, none of this should matter, but here is what you requested:
Red Hat Enterprise Linux Server 7.5 (Maipo)
Java(TM) SE Runtime Environment (build 1.8.0_112-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)
nextflow version 18.10.1.5003
singularity version 3.0.1 (Note that I don't use docker but singularity, also shouldn't matter)

@weinformatics
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Author

Not sure if it helps, none of this should matter, but here is what you requested:
Red Hat Enterprise Linux Server 7.5 (Maipo)
Java(TM) SE Runtime Environment (build 1.8.0_112-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)
nextflow version 18.10.1.5003
singularity version 3.0.1 (Note that I don't use docker but singularity, also shouldn't matter)

Thanks for your info. @d4straub In my case, I try singularity instead of Docker and then work.

@weinformatics
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Author

@d4straub I run the demo testdata and then an new issue occurs.

[cllcentos7@localhost ~]$ ./nextflow run nf-core/ampliseq -r 1.1.0 \
>     -profile singularity \
>     --reads "data" \
>     --FW_primer GTGYCAGCMGCCGCGGTAA \
>     --RV_primer GGACTACNVGGGTWTCTAAT \
>     --classifier "data/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-gg_13_8-85-qiime2_2019.7-classifier.qza" \
>     --metadata "data/Metadata.tsv" \
>     --max_cpus 4 \
>     --max_memory '40.GB'
N E X T F L O W  ~  version 19.07.0
Launching `nf-core/ampliseq` [exotic_varahamihira] - revision: 57e1ee2f90 [1.1.0]
[2m----------------------------------------------------
	                                ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
	                                `._,._,'
  nf-core/ampliseq v1.1.0
----------------------------------------------------
Pipeline Name     : nf-core/ampliseq
Pipeline Release  : 1.1.0
Run Name          : exotic_varahamihira
Reads             : data
Data Type         : Paired-End
Max Resources     : 40.GB memory, 4 cpus, 10d time per job
Container         : singularity - nfcore/ampliseq:1.1.0
Output dir        : ./results
Launch dir        : /home/cllcentos7
Working dir       : /home/cllcentos7/work
Script dir        : /home/cllcentos7/.nextflow/assets/nf-core/ampliseq
User              : cllcentos7
Config Profile    : singularity
[2m----------------------------------------------------
######## WARNING: No DADA2 cutoffs were specified, therefore reads will be truncated where median quality drops below 25.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.
executor >  local (13)
[92/ab2453] process > get_software_versions          [100%] 1 of 1 ✔
[9a/14f4aa] process > fastqc (1_S103_L001)           [ 75%] 3 of 4
[7a/5ad8d7] process > trimming (1a_S103_L001)        [100%] 4 of 4 ✔
[-        ] process > multiqc                        -
[df/dad73b] process > qiime_import (1)               [  0%] 0 of 1
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[81/5ce4e7] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[aa/af0c3c] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[cb/c40789] process > output_documentation (1)       [100%] 1 of 1 ✔
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import 					--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt 					--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
executor >  local (13)
[92/ab2453] process > get_software_versions          [100%] 1 of 1 ✔
[7a/41772c] process > fastqc (1a_S103_L001)          [100%] 4 of 4 ✔
[7a/5ad8d7] process > trimming (1a_S103_L001)        [100%] 4 of 4 ✔
[-        ] process > multiqc                        -
[df/dad73b] process > qiime_import (1)               [100%] 1 of 1, failed: 1 ✘
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[81/5ce4e7] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[aa/af0c3c] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[cb/c40789] process > output_documentation (1)       [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import 					--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt entos7/work/df/dad73b3e1505c3accf9bd--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
executor >  local (13)
[92/ab2453] process > get_software_versions          [100%] 1 of 1 ✔
[7a/41772c] process > fastqc (1a_S103_L001)          [100%] 4 of 4 ✔
[7a/5ad8d7] process > trimming (1a_S103_L001)        [100%] 4 of 4 ✔
[-        ] process > multiqc                        -
[df/dad73b] process > qiime_import (1)               [100%] 1 of 1, failed: 1 ✘
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[81/5ce4e7] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[aa/af0c3c] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[cb/c40789] process > output_documentation (1)       [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import rk/df/dad73b3e1505c3accf9bdc152b440--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt 					--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/q2_vsearch/plugin_setup.py", line 12, in <module>
      import q2_vsearch._cluster_features
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 15, in <module>
      import skbio
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/__init__.py", line 13, in <module>
      import skbio.io  # noqa
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/io/__init__.py", line 238, in <module>
      import_module('skbio.io.format.lsmat')
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/importlib/__init__.py", line 126, in import_module
      return _bootstrap._gcd_import(name[level:], package, level)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
      from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/stats/distance/__init__.py", line 192, in <module>
      from ._base import (DissimilarityMatrixError, DistanceMatrixError,
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 12, in <module>
      import matplotlib.pyplot as plt
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/pyplot.py", line 115, in <module>
      _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
      [backend_name], 0)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py", line 15, in <module>
      from .backend_qt5 import (
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/backend_qt5.py", line 19, in <module>
      import matplotlib.backends.qt_editor.figureoptions as figureoptions
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
      import matplotlib.backends.qt_editor.formlayout as formlayout
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 54, in <module>
      from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_compat.py", line 140, in <module>
      from PyQt5 import QtCore, QtGui, QtWidgets
  ImportError: libGL.so.1: cannot open shared object file: No such file or directory
  
  An unexpected error has occurred:
  
    libGL.so.1: cannot open shared object file: No such file or directory
  
  See above for debug info.

Work dir:
  /home/cllcentos7/work/df/dad73b3e1505c3accf9bdc152b4408

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[cllcentos7@localhost ~]$

@d4straub
Copy link
Collaborator

So last time docker didn't work as it should. Was on the right track after all.

The test run is typically started by this command:
nextflow run nf-core/ampliseq -r 1.1.0 -profile test,singularity
You do not need any other parameters, also no --max_memory or such.

@weinformatics
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weinformatics commented Sep 17, 2019 •
edited
Loading

So last time docker didn't work as it should. Was on the right track after all.

The test run is typically started by this command:
nextflow run nf-core/ampliseq -r 1.1.0 -profile test,singularity
You do not need any other parameters, also no --max_memory or such.

Still the same error by nextflow run nf-core/ampliseq -r 1.1.0 -profile test,singularity

[cllcentos7@localhost ~]$ ./nextflow run nf-core/ampliseq -r 1.1.0 -profile test,singularity
N E X T F L O W  ~  version 19.07.0
Launching `nf-core/ampliseq` [kickass_stallman] - revision: 57e1ee2f90 [1.1.0]
[2m----------------------------------------------------
	                                ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
	                                `._,._,'
  nf-core/ampliseq v1.1.0
----------------------------------------------------
Pipeline Name     : nf-core/ampliseq
Pipeline Release  : 1.1.0
Run Name          : kickass_stallman
Reads             : data/*_R{1,2}_001.fastq.gz
Data Type         : Paired-End
Max Resources     : 6 GB memory, 2 cpus, 2d time per job
Container         : singularity - nfcore/ampliseq:1.1.0
Output dir        : ./results
Launch dir        : /home/cllcentos7
Working dir       : /home/cllcentos7/work
Script dir        : /home/cllcentos7/.nextflow/assets/nf-core/ampliseq
User              : cllcentos7
Config Profile    : test,singularity
Config Description: Minimal test dataset to check pipeline function
[2m----------------------------------------------------
######## WARNING: No DADA2 cutoffs were specified, therefore reads will be truncated where median quality drops below 25.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.
executor >  local (14)
[d1/bd742a] process > get_software_versions          [100%] 1 of 1 ✔
[7f/281f93] process > fastqc (2a_S115)               [100%] 4 of 4 ✔
[bf/1ffbc3] process > trimming (2a_S115)             [100%] 4 of 4 ✔
[c3/ee72f6] process > multiqc                        [  0%] 0 of 1
[39/d6eb6d] process > qiime_import (1)               [  0%] 0 of 1
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[64/c9f22e] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[ca/ffbd7b] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[ef/8e67e7] process > output_documentation (1)       [100%] 1 of 1 ✔
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import 					--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt 					--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
executor >  local (14)
[d1/bd742a] process > get_software_versions          [100%] 1 of 1 ✔
[7f/281f93] process > fastqc (2a_S115)               [100%] 4 of 4 ✔
[bf/1ffbc3] process > trimming (2a_S115)             [100%] 4 of 4 ✔
[c3/ee72f6] process > multiqc                        [  0%] 0 of 1
[39/d6eb6d] process > qiime_import (1)               [100%] 1 of 1, failed: 1 ✘
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[64/c9f22e] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[ca/ffbd7b] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[ef/8e67e7] process > output_documentation (1)       [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import 					--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt 					--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
executor >  local (14)
[d1/bd742a] process > get_software_versions          [100%] 1 of 1 ✔
[7f/281f93] process > fastqc (2a_S115)               [100%] 4 of 4 ✔
[bf/1ffbc3] process > trimming (2a_S115)             [100%] 4 of 4 ✔
[c3/ee72f6] process > multiqc                        [100%] 1 of 1 ✔
[39/d6eb6d] process > qiime_import (1)               [100%] 1 of 1, failed: 1 ✘
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[64/c9f22e] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[ca/ffbd7b] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[ef/8e67e7] process > output_documentation (1)       [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import 					--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt entos7/work/39/d6eb6d75cc747c0b7b820--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
executor >  local (14)
[d1/bd742a] process > get_software_versions          [100%] 1 of 1 ✔
[7f/281f93] process > fastqc (2a_S115)               [100%] 4 of 4 ✔
[bf/1ffbc3] process > trimming (2a_S115)             [100%] 4 of 4 ✔
[c3/ee72f6] process > multiqc                        [100%] 1 of 1 ✔
[39/d6eb6d] process > qiime_import (1)               [100%] 1 of 1, failed: 1 ✘
[-        ] process > qiime_demux_visualize          -
[-        ] process > dada_trunc_parameter           -
[-        ] process > dada_single                    -
[-        ] process > classifier                     -
[-        ] process > filter_taxa                    -
[-        ] process > export_filtered_dada_output    -
[-        ] process > report_filter_stats            -
[-        ] process > RelativeAbundanceASV           -
[-        ] process > RelativeAbundanceReducedTaxa   -
[-        ] process > barplot                        -
[-        ] process > tree                           -
[-        ] process > alpha_rarefaction              -
[-        ] process > combinetable                   -
[-        ] process > diversity_core                 -
[64/c9f22e] process > metadata_category_all (1)      [100%] 1 of 1 ✔
[ca/ffbd7b] process > metadata_category_pairwise (1) [100%] 1 of 1 ✔
[-        ] process > alpha_diversity                -
[-        ] process > beta_diversity                 -
[-        ] process > beta_diversity_ordination      -
[-        ] process > prepare_ancom                  -
[-        ] process > ancom_tax                      -
[-        ] process > ancom_asv                      -
[ef/8e67e7] process > output_documentation (1)       [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import rk/39/d6eb6d75cc747c0b7b8209751bb2e--type 'SampleData[PairedEndSequencesWithQuality]' 					--input-path manifest.txt 					--output-path demux.qza 					--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/q2_vsearch/plugin_setup.py", line 12, in <module>
      import q2_vsearch._cluster_features
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 15, in <module>
      import skbio
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/__init__.py", line 13, in <module>
      import skbio.io  # noqa
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/io/__init__.py", line 238, in <module>
      import_module('skbio.io.format.lsmat')
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/importlib/__init__.py", line 126, in import_module
      return _bootstrap._gcd_import(name[level:], package, level)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
      from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/stats/distance/__init__.py", line 192, in <module>
      from ._base import (DissimilarityMatrixError, DistanceMatrixError,
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 12, in <module>
      import matplotlib.pyplot as plt
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/pyplot.py", line 115, in <module>
      _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
      [backend_name], 0)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py", line 15, in <module>
      from .backend_qt5 import (
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/backend_qt5.py", line 19, in <module>
      import matplotlib.backends.qt_editor.figureoptions as figureoptions
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
      import matplotlib.backends.qt_editor.formlayout as formlayout
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 54, in <module>
      from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_compat.py", line 140, in <module>
      from PyQt5 import QtCore, QtGui, QtWidgets
  ImportError: libGL.so.1: cannot open shared object file: No such file or directory
  
  An unexpected error has occurred:
  
    libGL.so.1: cannot open shared object file: No such file or directory
  
  See above for debug info.

Work dir:
  /home/cllcentos7/work/39/d6eb6d75cc747c0b7b8209751bb2e6

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[cllcentos7@localhost ~]$

@d4straub
Copy link
Collaborator

Same problem: libGL.so.1 seems part of it. Whats your singularity version? When singularity isn't properly set up this might happen, again @apeltzer would be the expert here ;)

@weinformatics
Copy link
Author

weinformatics commented Sep 17, 2019 •
edited
Loading

Same problem: libGL.so.1 seems part of it. Whats your singularity version? When singularity isn't properly set up this might happen, again @apeltzer would be the expert here ;)

The related softs version are listed as

[cllcentos7@localhost ~]$ uname -r
3.10.0-957.el7.x86_64
[cllcentos7@localhost ~]$ java -version
java version "1.8.0_212"
Java(TM) SE Runtime Environment (build 1.8.0_212-b10)
Java HotSpot(TM) 64-Bit Server VM (build 25.212-b10, mixed mode)
[cllcentos7@localhost ~]$ singularity version
3.4.0-1
[cllcentos7@localhost ~]$ docker -v
Docker version 19.03.2, build 6a30dfc
[cllcentos7@localhost ~]$

@weinformatics
Copy link
Author

Similarly, I run ./nextflow run nf-core/ampliseq -r 1.1.0 -profile test,docker to test the docker and still not work with the same error info.

[cllcentos7@localhost ~]$ ./nextflow run nf-core/ampliseq -r 1.1.0 -profile test,docker
N E X T F L O W  ~  version 19.07.0
Launching `nf-core/ampliseq` [condescending_cori] - revision: 57e1ee2f90 [1.1.0]
WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config
[2m----------------------------------------------------
	                                ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
	                                `._,._,'
  nf-core/ampliseq v1.1.0
----------------------------------------------------
Pipeline Name     : nf-core/ampliseq
Pipeline Release  : 1.1.0
Run Name          : condescending_cori
Reads             : data/*_R{1,2}_001.fastq.gz
Data Type         : Paired-End
Max Resources     : 6 GB memory, 2 cpus, 2d time per job
Container         : docker - nfcore/ampliseq:1.1.0
Output dir        : ./results
Launch dir        : /home/cllcentos7
Working dir       : /home/cllcentos7/work
Script dir        : /home/cllcentos7/.nextflow/assets/nf-core/ampliseq
User              : cllcentos7
Config Profile    : test,docker
Config Description: Minimal test dataset to check pipeline function
[2m----------------------------------------------------
######## WARNING: No DADA2 cutoffs were specified, therefore reads will be truncated where median quality drops below 25.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.
executor >  local (2)
[fb/a17373] process > get_software_versions        [  0%] 0 of 1
[-        ] process > fastqc                       -
[-        ] process > trimming                     -
[-        ] process > multiqc                      -
[-        ] process > qiime_import                 -
[-        ] process > qiime_demux_visualize        -
[-        ] process > dada_trunc_parameter         -
[-        ] process > dada_single                  -
[-        ] process > classifier                   -
[-        ] process > filter_taxa                  -
[-        ] process > export_filtered_dada_output  -
[-        ] process > report_filter_stats          -
[-        ] process > RelativeAbundanceASV         -
[-        ] process > RelativeAbundanceReducedTaxa -
[-        ] process > barplot                      -
[-        ] process > tree                         -
[-        ] process > alpha_rarefaction            -
[-        ] process > combinetable                 -
[-        ] process > diversity_core               -
executor >  local (2)
[fb/a17373] process > get_software_versions        [100%] 1 of 1, failed: 1 ✘
[-        ] process > fastqc                       -
[-        ] process > trimming                     -
[-        ] process > multiqc                      -
[-        ] process > qiime_import                 -
[-        ] process > qiime_demux_visualize        -
[-        ] process > dada_trunc_parameter         -
[-        ] process > dada_single                  -
[-        ] process > classifier                   -
[-        ] process > filter_taxa                  -
[-        ] process > export_filtered_dada_output  -
[-        ] process > report_filter_stats          -
[-        ] process > RelativeAbundanceASV         -
[-        ] process > RelativeAbundanceReducedTaxa -
[-        ] process > barplot                      -
[-        ] process > tree                         -
[-        ] process > alpha_rarefaction            -
[-        ] process > combinetable                 -
[-        ] process > diversity_core               -
[-        ] process > metadata_category_all        -
[-        ] process > metadata_category_pairwise   -
executor >  local (2)
[fb/a17373] process > get_software_versions        [100%] 1 of 1, failed: 1 ✘
[-        ] process > fastqc                       -
[-        ] process > trimming                     -
[-        ] process > multiqc                      -
[-        ] process > qiime_import                 -
[-        ] process > qiime_demux_visualize        -
[-        ] process > dada_trunc_parameter         -
[-        ] process > dada_single                  -
[-        ] process > classifier                   -
[-        ] process > filter_taxa                  -
[-        ] process > export_filtered_dada_output  -
[-        ] process > report_filter_stats          -
[-        ] process > RelativeAbundanceASV         -
[-        ] process > RelativeAbundanceReducedTaxa -
[-        ] process > barplot                      -
[-        ] process > tree                         -
[-        ] process > alpha_rarefaction            -
[-        ] process > combinetable                 -
[-        ] process > diversity_core               -
[-        ] process > metadata_category_all        -
[-        ] process > metadata_category_pairwise   -
[-        ] process > alpha_diversity              -
[-        ] process > beta_diversity               -
[-        ] process > beta_diversity_ordination    -
[-        ] process > prepare_ancom                -
[-        ] process > ancom_tax                    -
[-        ] process > ancom_asv                    -
[a0/bba1e7] process > output_documentation (1)     [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (1)

Command executed:

  echo 1.1.0 > v_pipeline.txt
  echo 19.07.0 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  cutadapt --version > v_cutadapt.txt
  qiime --version > v_qiime.txt
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: IPv4 forwarding is disabled. Networking will not work.
  .command.run: line 186: uname: command not found
  .command.run: line 138: grep: command not found
  .command.run: line 139: grep: command not found
  .command.run: line 200: date: command not found
  Command 'ps' required by nextflow to collect task metrics cannot be found

Work dir:
  /home/cllcentos7/work/fb/a1737336329d4a8d7cb6f25a256480

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[cllcentos7@localhost ~]$

@d4straub
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That looks like a different error to me.

  • with docker there is no access to any programs of the container.
  • with singularity "only" a shared library, namely libGL.so.1, is not accessible.

@weinformatics
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weinformatics commented Sep 17, 2019 •
edited
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That looks like a different error to me.

  • with docker there is no access to any programs of the container.
  • with singularity "only" a shared library, namely libGL.so.1, is not accessible.

Yes. You are right. docker and singularity are independent.
It seems to me that nf-core pipelines may need to run fine at a right version env of docker, nextflow, singularity or java. Let me try your #102 (comment) and this will give the answer.

@weinformatics
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weinformatics commented Sep 26, 2019 •
edited
Loading

That looks like a different error to me.

  • with docker there is no access to any programs of the container.
  • with singularity "only" a shared library, namely libGL.so.1, is not accessible.

Yes. You are right. docker and singularity are independent.
It seems to me that nf-core pipelines may need to run fine at a right version env of docker, nextflow, singularity or java. Let me try your #102 (comment) and this will give the answer.

@d4straub @apeltzer Sorry for the delay reply. From my side I need anyone's help. I try the singularity version 3.0.1 and still can not work as

Execution cancelled -- Finishing pending tasks before exit
[0;35m[nf-core/ampliseq] Pipeline completed with errors
Error executing process > 'qiime_import (1)'

Caused by:
  Process `qiime_import (1)` terminated with an error exit status (1)

Command executed:

  qiime tools import envs/nf-core-ampliseq-1.1.0/lib/pyt--type 'SampleData[PairedEndSequencesWithQuality]' formlayout.py", line 54, in <module> --input-path manifest.txt 					--output-path demux.qza from matplotlib.backends.qt_compat--source-format PairedEndFastqManifestPhred33

Command exit status:
  1

Command output:
  (empty)

Command error:
      view_type=source_format)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/result.py", line 182, in import_data
      type_ = qiime2.sdk.parse_type(type_)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
      pm = qiime2.sdk.PluginManager()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
      self._init()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
      plugin = entry_point.load()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2318, in load
      return self.resolve()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2324, in resolve
      module = __import__(self.module_name, fromlist=['__name__'], level=0)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/q2_vsearch/plugin_setup.py", line 12, in <module>
      import q2_vsearch._cluster_features
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 15, in <module>
      import skbio
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/__init__.py", line 13, in <module>
      import skbio.io  # noqa
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/io/__init__.py", line 238, in <module>
      import_module('skbio.io.format.lsmat')
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/importlib/__init__.py", line 126, in import_module
      return _bootstrap._gcd_import(name[level:], package, level)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
      from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/stats/distance/__init__.py", line 192, in <module>
      from ._base import (DissimilarityMatrixError, DistanceMatrixError,
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 12, in <module>
      import matplotlib.pyplot as plt
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/pyplot.py", line 115, in <module>
      _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
      [backend_name], 0)
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py", line 15, in <module>
      from .backend_qt5 import (
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/backend_qt5.py", line 19, in <module>
      import matplotlib.backends.qt_editor.figureoptions as figureoptions
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
      import matplotlib.backends.qt_editor.formlayout as formlayout
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 54, in <module>
      from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
    File "/opt/conda/envs/nf-core-ampliseq-1.1.0/lib/python3.5/site-packages/matplotlib/backends/qt_compat.py", line 140, in <module>
      from PyQt5 import QtCore, QtGui, QtWidgets
  ImportError: libGL.so.1: cannot open shared object file: No such file or directory
  
  An unexpected error has occurred:
  
    libGL.so.1: cannot open shared object file: No such file or directory
  
  See above for debug info.

Work dir:
  /home/cllcentos8/work/88/f98b956a9067c0f7954db520084652

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

I suspect It was caused by basic OS so I test on Debian 9. Even still can not work but libGL.so.1: cannot open shared object file: No such file or directory error gone. As is show :

clldebian9@clldebian9:~$ sudo ./nextflow run nf-core/ampliseq -r 1.0.0 -profile test,singularity
N E X T F L O W  ~  version 19.07.0
Launching `nf-core/ampliseq` [desperate_babbage] - revision: f0357d61cf [1.0.0]
=======================================================
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~'
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

nf-core/ampliseq v1.0.0"
=======================================================
Pipeline Name  : nf-core/ampliseq
Pipeline Version: 1.0.0
Run Name       : desperate_babbage
Reads          : data/*_L001_R{1,2}_001.fastq.gz
Max Memory     : 6 GB
Max CPUs       : 2
Max Time       : 2d
Output dir     : ./results
Working dir    : /home/clldebian9/work
Container Engine: singularity
Container      : nfcore/ampliseq:1.0.0
Current home   : /root
Current user   : root
Current path   : /home/clldebian9
Script dir     : /root/.nextflow/assets/nf-core/ampliseq
Config Profile : test,singularity
=========================================
executor >  local (2)
[69/ea0d8c] process > get_software_versions        [  0%] 0 of 1
executor >  local (2)
[69/ea0d8c] process > get_software_versions        [100%] 1 of 1, failed: 1 ✘
[-        ] process > fastqc                       -
executor >  local (2)
[69/ea0d8c] process > get_software_versions        [100%] 1 of 1, failed: 1 ✘
[-        ] process > fastqc                       -
[-        ] process > trimming                     -
executor >  local (2)
[69/ea0d8c] process > get_software_versions        [100%] 1 of 1, failed: 1 ✘
[-        ] process > fastqc                       -
[-        ] process > trimming                     -
[-        ] process > multiqc                      -
[-        ] process > qiime_import                 -
[-        ] process > qiime_demux_visualize        -
[-        ] process > dada_trunc_parameter         -
[-        ] process > dada_single                  -
[-        ] process > classifier                   -
[-        ] process > filter_taxa                  -
[-        ] process > export_filtered_dada_output  -
[-        ] process > report_filter_stats          -
[-        ] process > RelativeAbundanceASV         -
[-        ] process > RelativeAbundanceReducedTaxa -
[-        ] process > barplot                      -
[-        ] process > tree                         -
[-        ] process > alpha_rarefaction            -
[-        ] process > combinetable                 -
[-        ] process > diversity_core               -
[-        ] process > metadata_category_all        -
[-        ] process > metadata_category_pairwise   -
[-        ] process > alpha_diversity              -
[-        ] process > beta_diversity               -
[-        ] process > beta_diversity_ordination    -
[-        ] process > prepare_ancom                -
[-        ] process > ancom_tax                    -
[-        ] process > ancom_asv                    -
[80/c284b6] process > output_documentation (1)     [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
[nf-core/ampliseq] Pipeline Complete
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (127)

Command executed:

  echo 1.0.0 > v_pipeline.txt
  echo 19.07.0 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  scrape_software_versions.py > software_versions_mqc.yaml

Command exit status:
  127

Command output:
  (empty)

Command error:
  /bin/bash: line 0: cd: /home/clldebian9/work/69/ea0d8cdfe372e545a4a649906d19dd: No such file or directory
  /bin/bash: .command.run: No such file or directory

Work dir:
  /home/clldebian9/work/69/ea0d8cdfe372e545a4a649906d19dd

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

clldebian9@clldebian9:~$

@d4straub
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With basic OS the container somehow cannot access the shared library which is available in the container. I am no expert here, but this shouldn't happen, I have no lead what could cause it.

With Debian 9 there seems to be no access to the folder system, meaning singularity has no access. This leads to the suspicion that singularity isn't installed properly.

@weinformatics
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Author

weinformatics commented Sep 26, 2019 •
edited
Loading

With basic OS the container somehow cannot access the shared library which is available in the container. I am no expert here, but this shouldn't happen, I have no lead what could cause it.

With Debian 9 there seems to be no access to the folder system, meaning singularity has no access. This leads to the suspicion that singularity isn't installed properly.

Okay. I got it. I am trying on potential test. @d4straub Pipeline completed successfully on centos 7.5 and #102 (comment) but which cause this issue still unknown. Even I haven't test other pipelines, I think ENVs should be provided along with every nf-core pipelines. Now you can close this issue.

@weinformatics
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Author

Not sure if it helps, none of this should matter, but here is what you requested:
Red Hat Enterprise Linux Server 7.5 (Maipo)
Java(TM) SE Runtime Environment (build 1.8.0_112-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)
nextflow version 18.10.1.5003
singularity version 3.0.1 (Note that I don't use docker but singularity, also shouldn't matter)

Thanks for your info. @d4straub In my case, I try singularity instead of Docker and then work.

@d4straub I just wander a suitable docker version. Can you tell me which your team was using now ?

@d4straub
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We are not using docker but singularity to execute pipelines.

@weinformatics
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We are not using docker but singularity to execute pipelines.

Thanks for your reply !!!

@bschilder bschilder mentioned this issue Jan 21, 2021
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@d4straub @weinformatics