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Add ncov-recombinant v0.6.1 APHL Docker Workshop #583

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@whottel whottel commented Feb 7, 2023

This PR is for ncov-recombinant version 0.6.1. The dockerfile uses micromamba as the base image.

Pull Request (PR) checklist:

  • [X ] Include a description of what is in this pull request in this message.
  • [ X] The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
  • [X ] Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • [X ] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • [X ] Dockerfile includes the recommended LABELS
  • [X ] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • [X ] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

Comment on lines 19 to 22
RUN apt-get update && apt-get install -y python \
git \
wget && \
rm -rf /var/lib/apt/lists/* && apt-get autoclean
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We have found that images are smaller when using --no-install-recommends

Could you adjust line 19 to

apt-get update && apt-get install --no-install-recommends -y python \

Comment on lines 25 to 26
RUN git clone https://github.com/ktmeaton/ncov-recombinant.git &&\
cd ncov-recombinant
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Instead of using git clone, could you download the tarball for the version you are creating an image for?

# something like
wget https://github.com/ktmeaton/ncov-recombinant/archive/refs/tags/v0.6.1.tar.gz

git clone is hard for version control

You image will also likely be smaller and more stable if you download the tarball and install it from that as well (instead of using micromamba). Did you already try that?

@erinyoung erinyoung added the workshop Part of a training workshop label Feb 8, 2023
@erinyoung
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Your Dockerfile built successfully and your test worked.

I was going to copy the results of the tests, but it's a lot of lines.

Github actions failed because your image is missing ps - which can be easily remedied by installing procps in your apt-get layer.

@erinyoung
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Were you able to get your permissions issues figured out?

@whottel
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whottel commented Feb 16, 2023

Unfortunately, I am still getting errors.
Attempting to recreate what you mentioned on Slack
Running the command
docker run --rm -v ${PWD}:/data ncov:test3 snakemake --profile /ncov-recombinant-0.6.1/profiles/controls-positive
still results in the following error:
Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile.

When I explicitly state where the Snakefile should be with
docker run --rm -v ${PWD}:/data ncov:test3 snakemake --profile /ncov-recombinant-0.6.1/profiles/controls-positive --snakefile /ncov-recombinant-0.6.1/workflow/Snakefile

I get this error:

 /ncov-recombinant-0.6.1/workflow/Snakefile
Traceback (most recent call last):
  File "/opt/conda/envs/ncov-recombinant-env/bin/snakemake", line 10, in <module>
    sys.exit(main())
  File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/snakemake/__init__.py", line 2803, in main
    success = snakemake(
  File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/snakemake/__init__.py", line 513, in snakemake
    update_config(overwrite_config, load_configfile(f))
  File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/snakemake/io.py", line 1640, in load_configfile
    config = _load_configfile(configpath)
  File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/snakemake/io.py", line 1605, in _load_configfile
    obj = open(configpath_or_obj, encoding="utf-8")
FileNotFoundError: [Errno 2] No such file or directory: 'defaults/parameters.yaml'

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I was working on this today, and I actually got this to work (to a point). I tried to run the tutorial, but there's something wrong with a python script included in the repo (I keep getting type errors when I run the tutorial or other profiles).

I'm currently on the mindset that we should wait until https://github.com/phac-nml/rebar has a released version and close this PR.

 > [test 3/3] RUN snakemake --profile /ncov-recombinant/profiles/tutorial:                                                                                                                                                                                                                                             
#0 1.547 Config file defaults/parameters.yaml is extended by additional config specified via the command line.                                                                                                                                                                                                         
#0 1.556 Building DAG of jobs...                                                                                                                                                                                                                                                                                       
#0 1.595 Using shell: /bin/bash                                                                                                                                                                                                                                                                                        
#0 1.595 Provided cores: 1 (use --cores to define parallelism)                                                                                                                                                                                                                                                         
#0 1.595 Rules claiming more threads will be scaled down.
#0 1.606 Job stats:
#0 1.606 job                   count    min threads    max threads
#0 1.606 ------------------  -------  -------------  -------------
#0 1.606 all                       1              1              1
#0 1.606 linelist                  1              1              1
#0 1.606 nextclade                 3              1              1
#0 1.606 nextclade_dataset         3              1              1
#0 1.606 plot                      4              1              1
#0 1.606 rbd_levels                1              1              1
#0 1.606 report                    4              1              1
#0 1.606 save_config               1              1              1
#0 1.606 sc2rf                    12              1              1
#0 1.606 sc2rf_recombinants        1              1              1
#0 1.606 summary                   1              1              1
#0 1.606 validate                  1              1              1
#0 1.606 total                    33              1              1
#0 1.606 
#0 1.606 Select jobs to execute...
#0 1.668 
#0 1.668 [Tue Jul 18 16:34:57 2023]
#0 1.668 Job 3: Downloading Nextclade dataset.
#0 1.668 
#0 1.668   log:     logs/nextclade_dataset/sars-cov-2_2023-02-01T12:00:00Z_2023-07-18.log
#0 1.668   dataset: data/sars-cov-2_2023-02-01T12:00:00Z
#0 1.668   
#0 1.668 
#0 3.545 [Tue Jul 18 16:34:59 2023]
#0 3.545 Finished job 3.
#0 3.545 1 of 33 steps (3%) done
#0 3.545 Select jobs to execute...
#0 3.574 
#0 3.574 [Tue Jul 18 16:34:59 2023]
#0 3.574 Job 27: Downloading Nextclade dataset.
#0 3.574 
#0 3.574   log:     logs/nextclade_dataset/sars-cov-2-21L_2023-02-01T12:00:00Z_2023-07-18.log
#0 3.574   dataset: data/sars-cov-2-21L_2023-02-01T12:00:00Z
#0 3.574   
#0 3.574 
#0 4.881 [Tue Jul 18 16:35:00 2023]
#0 4.881 Finished job 27.
#0 4.881 2 of 33 steps (6%) done
#0 4.882 Select jobs to execute...
#0 4.909 
#0 4.909 [Tue Jul 18 16:35:00 2023]
#0 4.909 Job 26: Aligning sequences and performing QC with Nextclade.
#0 4.909 
#0 4.909   build:     tutorial
#0 4.909   log:       logs/nextclade_immune-escape/tutorial_2023-07-18.log
#0 4.909   qc:        results/tutorial/nextclade_immune-escape/qc.tsv
#0 4.909   metadata:  results/tutorial/nextclade_immune-escape/metadata.tsv
#0 4.909   alignment: results/tutorial/nextclade_immune-escape/alignment.fasta
#0 4.909   
#0 4.909 
#0 5.153 [Tue Jul 18 16:35:00 2023]
#0 5.153 Finished job 26.
#0 5.153 3 of 33 steps (9%) done
#0 5.154 Select jobs to execute...
#0 5.181 
#0 5.181 [Tue Jul 18 16:35:00 2023]
#0 5.181 Job 1: Saving full config.
#0 5.181 
#0 6.201 [Tue Jul 18 16:35:01 2023]
#0 6.201 Finished job 1.
#0 6.201 4 of 33 steps (12%) done
#0 6.202 Select jobs to execute...
#0 6.229 
#0 6.229 [Tue Jul 18 16:35:01 2023]
#0 6.229 Job 25: Calculating the number of key RBD mutations.
#0 6.229 
#0 6.229   build:     tutorial
#0 6.229   log:       logs/rbd_levels/tutorial_2023-07-18.log
#0 6.229   table:     results/tutorial/rbd_levels/rbd_levels.tsv
#0 6.229   
#0 6.229 
#0 7.314 [Tue Jul 18 16:35:02 2023]
#0 7.314 Finished job 25.
#0 7.314 5 of 33 steps (15%) done
#0 7.315 Select jobs to execute...
#0 7.341 
#0 7.341 [Tue Jul 18 16:35:02 2023]
#0 7.341 Job 19: Downloading Nextclade dataset.
#0 7.341 
#0 7.341   log:     logs/nextclade_dataset/sars-cov-2-no-recomb_2023-02-01T12:00:00Z_2023-07-18.log
#0 7.341   dataset: data/sars-cov-2-no-recomb_2023-02-01T12:00:00Z
#0 7.341   
#0 7.341 
#0 8.676 [Tue Jul 18 16:35:04 2023]
#0 8.676 Finished job 19.
#0 8.677 6 of 33 steps (18%) done
#0 8.677 Select jobs to execute...
#0 8.707 
#0 8.707 [Tue Jul 18 16:35:04 2023]
#0 8.707 Job 2: Aligning sequences and performing QC with Nextclade.
#0 8.707 
#0 8.707   build:     tutorial
#0 8.707   log:       logs/nextclade/tutorial_2023-07-18.log
#0 8.707   qc:        results/tutorial/nextclade/qc.tsv
#0 8.707   metadata:  results/tutorial/nextclade/metadata.tsv
#0 8.707   alignment: results/tutorial/nextclade/alignment.fasta
#0 8.707   
#0 8.707 
#0 9.856 [Tue Jul 18 16:35:05 2023]
#0 9.856 Finished job 2.
#0 9.856 7 of 33 steps (21%) done
#0 9.857 Select jobs to execute...
#0 9.887 
#0 9.887 [Tue Jul 18 16:35:05 2023]
#0 9.887 Job 6: Identifying recombinants with sc2rf.
#0 9.887 
#0 9.887   mode:        XB
#0 9.887   build:       tutorial
#0 9.887   log:         logs/sc2rf/tutorial_XB_2023-07-18.log
#0 9.887   ansi:        results/tutorial/sc2rf/ansi.XB.txt
#0 9.887   stats:       results/tutorial/sc2rf/stats.XB.csv
#0 9.887   
#0 9.887 
#0 10.23 [Tue Jul 18 16:35:05 2023]
#0 10.23 Finished job 6.
#0 10.23 8 of 33 steps (24%) done
#0 10.23 Select jobs to execute...
#0 10.26 
#0 10.26 [Tue Jul 18 16:35:05 2023]
#0 10.26 Job 8: Identifying recombinants with sc2rf.
#0 10.26 
#0 10.26   mode:        proposed808
#0 10.26   build:       tutorial
#0 10.26   log:         logs/sc2rf/tutorial_proposed808_2023-07-18.log
#0 10.26   ansi:        results/tutorial/sc2rf/ansi.proposed808.txt
#0 10.26   stats:       results/tutorial/sc2rf/stats.proposed808.csv
#0 10.26   
#0 10.26 
#0 10.58 [Tue Jul 18 16:35:06 2023]
#0 10.58 Finished job 8.
#0 10.58 9 of 33 steps (27%) done
#0 10.58 Select jobs to execute...
#0 10.61 
#0 10.61 [Tue Jul 18 16:35:06 2023]
#0 10.61 Job 10: Identifying recombinants with sc2rf.
#0 10.61 
#0 10.61   mode:        XAY_XBA_XBC
#0 10.61   build:       tutorial
#0 10.61   log:         logs/sc2rf/tutorial_XAY_XBA_XBC_2023-07-18.log
#0 10.61   ansi:        results/tutorial/sc2rf/ansi.XAY_XBA_XBC.txt
#0 10.61   stats:       results/tutorial/sc2rf/stats.XAY_XBA_XBC.csv
#0 10.61   
#0 10.61 
#0 10.93 [Tue Jul 18 16:35:06 2023]
#0 10.93 Finished job 10.
#0 10.93 10 of 33 steps (30%) done
#0 10.93 Select jobs to execute...
#0 10.96 
#0 10.96 [Tue Jul 18 16:35:06 2023]
#0 10.96 Job 12: Identifying recombinants with sc2rf.
#0 10.96 
#0 10.96   mode:        delta_omicron
#0 10.96   build:       tutorial
#0 10.96   log:         logs/sc2rf/tutorial_delta_omicron_2023-07-18.log
#0 10.96   ansi:        results/tutorial/sc2rf/ansi.delta_omicron.txt
#0 10.96   stats:       results/tutorial/sc2rf/stats.delta_omicron.csv
#0 10.96   
#0 10.96 
#0 11.29 [Tue Jul 18 16:35:06 2023]
#0 11.29 Finished job 12.
#0 11.29 11 of 33 steps (33%) done
#0 11.29 Select jobs to execute...
#0 11.32 
#0 11.32 [Tue Jul 18 16:35:06 2023]
#0 11.32 Job 18: Aligning sequences and performing QC with Nextclade.
#0 11.32 
#0 11.32   build:     tutorial
#0 11.32   log:       logs/nextclade_no-recomb/tutorial_2023-07-18.log
#0 11.32   qc:        results/tutorial/nextclade_no-recomb/qc.tsv
#0 11.32   metadata:  results/tutorial/nextclade_no-recomb/metadata.tsv
#0 11.32   alignment: results/tutorial/nextclade_no-recomb/alignment.fasta
#0 11.32   
#0 11.32 
#0 11.58 [Tue Jul 18 16:35:07 2023]
#0 11.58 Finished job 18.
#0 11.58 12 of 33 steps (36%) done
#0 11.58 Select jobs to execute...
#0 11.60 
#0 11.60 [Tue Jul 18 16:35:07 2023]
#0 11.60 Job 16: Identifying recombinants with sc2rf.
#0 11.60 
#0 11.60   mode:        voc-2023
#0 11.60   build:       tutorial
#0 11.60   log:         logs/sc2rf/tutorial_voc-2023_2023-07-18.log
#0 11.60   ansi:        results/tutorial/sc2rf/ansi.voc-2023.txt
#0 11.60   stats:       results/tutorial/sc2rf/stats.voc-2023.csv
#0 11.60   
#0 11.60 
#0 11.92 [Tue Jul 18 16:35:07 2023]
#0 11.92 Finished job 16.
#0 11.92 13 of 33 steps (39%) done
#0 11.92 Select jobs to execute...
#0 11.95 
#0 11.95 [Tue Jul 18 16:35:07 2023]
#0 11.95 Job 13: Identifying recombinants with sc2rf.
#0 11.95 
#0 11.95   mode:        omicron_omicron
#0 11.95   build:       tutorial
#0 11.95   log:         logs/sc2rf/tutorial_omicron_omicron_2023-07-18.log
#0 11.95   ansi:        results/tutorial/sc2rf/ansi.omicron_omicron.txt
#0 11.95   stats:       results/tutorial/sc2rf/stats.omicron_omicron.csv
#0 11.95   
#0 11.95 
#0 12.28 [Tue Jul 18 16:35:07 2023]
#0 12.28 Finished job 13.
#0 12.28 14 of 33 steps (42%) done
#0 12.28 Select jobs to execute...
#0 12.30 
#0 12.30 [Tue Jul 18 16:35:07 2023]
#0 12.30 Job 11: Identifying recombinants with sc2rf.
#0 12.30 
#0 12.30   mode:        XBB
#0 12.30   build:       tutorial
#0 12.30   log:         logs/sc2rf/tutorial_XBB_2023-07-18.log
#0 12.30   ansi:        results/tutorial/sc2rf/ansi.XBB.txt
#0 12.30   stats:       results/tutorial/sc2rf/stats.XBB.csv
#0 12.30   
#0 12.30 
#0 12.63 [Tue Jul 18 16:35:08 2023]
#0 12.63 Finished job 11.
#0 12.63 15 of 33 steps (45%) done
#0 12.63 Select jobs to execute...
#0 12.65 
#0 12.65 [Tue Jul 18 16:35:08 2023]
#0 12.65 Job 9: Identifying recombinants with sc2rf.
#0 12.65 
#0 12.65   mode:        XAJ
#0 12.65   build:       tutorial
#0 12.65   log:         logs/sc2rf/tutorial_XAJ_2023-07-18.log
#0 12.65   ansi:        results/tutorial/sc2rf/ansi.XAJ.txt
#0 12.65   stats:       results/tutorial/sc2rf/stats.XAJ.csv
#0 12.65   
#0 12.65 
#0 12.98 [Tue Jul 18 16:35:08 2023]
#0 12.98 Finished job 9.
#0 12.98 16 of 33 steps (48%) done
#0 12.98 Select jobs to execute...
#0 13.04 
#0 13.04 [Tue Jul 18 16:35:08 2023]
#0 13.04 Job 15: Identifying recombinants with sc2rf.
#0 13.04 
#0 13.04   mode:        voc-2022-CJ
#0 13.04   build:       tutorial
#0 13.04   log:         logs/sc2rf/tutorial_voc-2022-CJ_2023-07-18.log
#0 13.04   ansi:        results/tutorial/sc2rf/ansi.voc-2022-CJ.txt
#0 13.04   stats:       results/tutorial/sc2rf/stats.voc-2022-CJ.csv
#0 13.04   
#0 13.04 
#0 13.36 [Tue Jul 18 16:35:08 2023]
#0 13.36 Finished job 15.
#0 13.36 17 of 33 steps (52%) done
#0 13.36 Select jobs to execute...
#0 13.38 
#0 13.39 [Tue Jul 18 16:35:08 2023]
#0 13.39 Job 7: Identifying recombinants with sc2rf.
#0 13.39 
#0 13.39   mode:        XC
#0 13.39   build:       tutorial
#0 13.39   log:         logs/sc2rf/tutorial_XC_2023-07-18.log
#0 13.39   ansi:        results/tutorial/sc2rf/ansi.XC.txt
#0 13.39   stats:       results/tutorial/sc2rf/stats.XC.csv
#0 13.39   
#0 13.39 
#0 13.71 [Tue Jul 18 16:35:09 2023]
#0 13.71 Finished job 7.
#0 13.71 18 of 33 steps (55%) done
#0 13.71 Select jobs to execute...
#0 13.74 
#0 13.74 [Tue Jul 18 16:35:09 2023]
#0 13.74 Job 5: Identifying recombinants with sc2rf.
#0 13.74 
#0 13.74   mode:        XA
#0 13.74   build:       tutorial
#0 13.74   log:         logs/sc2rf/tutorial_XA_2023-07-18.log
#0 13.74   ansi:        results/tutorial/sc2rf/ansi.XA.txt
#0 13.74   stats:       results/tutorial/sc2rf/stats.XA.csv
#0 13.74   
#0 13.74 
#0 14.05 [Tue Jul 18 16:35:09 2023]
#0 14.05 Finished job 5.
#0 14.05 19 of 33 steps (58%) done
#0 14.05 Select jobs to execute...
#0 14.05 
#0 14.05 [Tue Jul 18 16:35:09 2023]
#0 14.05 Job 14: Identifying recombinants with sc2rf.
#0 14.05 
#0 14.05   mode:        voc-2022
#0 14.05   build:       tutorial
#0 14.05   log:         logs/sc2rf/tutorial_voc-2022_2023-07-18.log
#0 14.05   ansi:        results/tutorial/sc2rf/ansi.voc-2022.txt
#0 14.05   stats:       results/tutorial/sc2rf/stats.voc-2022.csv
#0 14.05   
#0 14.05 
#0 14.38 [Tue Jul 18 16:35:09 2023]
#0 14.38 Finished job 14.
#0 14.38 20 of 33 steps (61%) done
#0 14.38 Select jobs to execute...
#0 14.38 
#0 14.38 [Tue Jul 18 16:35:09 2023]
#0 14.38 Job 4: Postprocessing the sc2rf output to identify recombinants.
#0 14.38 
#0 14.38   build:       tutorial
#0 14.38   log:         logs/sc2rf_recombinants/tutorial_2023-07-18.log
#0 14.38   stats:       results/tutorial/sc2rf/stats.tsv
#0 14.38   alignment:   results/tutorial/sc2rf/recombinants.fasta
#0 14.38   ansi:        results/tutorial/sc2rf/recombinants.ansi.txt
#0 14.38   
#0 14.38 
#0 34.74 [Tue Jul 18 16:35:30 2023]
#0 34.74 Finished job 4.
#0 34.74 21 of 33 steps (64%) done
#0 34.74 Select jobs to execute...
#0 34.74 
#0 34.74 [Tue Jul 18 16:35:30 2023]
#0 34.74 Job 24: Summarizing results from pipeline tools.
#0 34.74 
#0 34.74   build:      tutorial
#0 34.74   log:        logs/summary/tutorial_2023-07-18.log
#0 34.74   summary:    results/tutorial/linelists/summary.tsv
#0 34.74   
#0 34.74 
#0 34.80 [Tue Jul 18 16:35:30 2023]
#0 34.80 Finished job 24.
#0 34.80 22 of 33 steps (67%) done
#0 34.80 Select jobs to execute...
#0 34.80 
#0 34.80 [Tue Jul 18 16:35:30 2023]
#0 34.80 Job 23: Creating linelists of recombinant sequences, lineages, and parents.
#0 34.80 
#0 34.80   build:             tutorial
#0 34.80   log:               logs/linelist/tutorial_2023-07-18.log
#0 34.80   positives:         results/tutorial/linelists/positives.tsv
#0 34.80   negatives:         results/tutorial/linelists/negatives.tsv
#0 34.80   false_positives:   results/tutorial/linelists/false_positives.tsv
#0 34.80   lineages:          results/tutorial/linelists/lineages.tsv
#0 34.80   parents:           results/tutorial/linelists/parents.tsv
#0 34.80   
#0 34.80 
#0 36.39 [Tue Jul 18 16:35:31 2023]
#0 36.39 Finished job 23.
#0 36.39 23 of 33 steps (70%) done
#0 36.39 Select jobs to execute...
#0 36.42 
#0 36.42 [Tue Jul 18 16:35:31 2023]
#0 36.42 Job 22: Plotting results.
#0 36.42 
#0 36.42   build:   tutorial
#0 36.42   log:     logs/plots/tutorial_2023-07-18.log
#0 36.42   plots:   results/tutorial/plots
#0 36.42   
#0 36.42 
#0 37.21 [Tue Jul 18 16:35:32 2023]
#0 37.21 Error in rule plot:
#0 37.21     jobid: 22
#0 37.21     output: results/tutorial/plots
#0 37.21     log: logs/plots/tutorial_2023-07-18.log (check log file(s) for error message)
#0 37.21     shell:
#0 37.21         
#0 37.21     python3 scripts/plot.py       --input results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots       --lag 4       --geo country       --weeks 16       --min-date 2022-02-09       --max-date 2022-07-04       --min-cluster-size 1       > logs/plots/tutorial_2023-07-18.log 2>&1;
#0 37.21 
#0 37.21     # Extract the cluster IDs to be plotted
#0 37.21     cluster_ids=$(csvtk headers -t results/tutorial/plots/cluster_id.tsv | tail -n+2 | tr "\n" "," | sed 's/,$/\n/g')
#0 37.21 
#0 37.21     # Plot breakpoints by clade
#0 37.21     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots       --parent-col parents_clade       --parent-type clade       --cluster-col cluster_id       --clusters "${cluster_ids}"              >> logs/plots/tutorial_2023-07-18.log 2>&1;
#0 37.21 
#0 37.21     # Plot breakpoints by lineage
#0 37.21     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots       --parent-col parents_lineage       --parent-type lineage       --cluster-col cluster_id       --clusters "${cluster_ids}"              >> logs/plots/tutorial_2023-07-18.log 2>&1;
#0 37.21     
#0 37.21         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
#0 37.21 Logfile logs/plots/tutorial_2023-07-18.log:
#0 37.21 Importing linelist: results/tutorial/linelists/positives.tsv
#0 37.21 Filtering on data
#0 37.21 Creating pivot tables
#0 37.21 Creating plot data: lineage
#0 37.21 Creating plot data: status
#0 37.21 Creating plot data: geography
#0 37.21 Creating plot data: largest
#0 37.21 Creating plot data: designated
#0 37.21 Creating plot data: proposed
#0 37.21 Creating plot data: unpublished
#0 37.21 Creating plot data: parents_clade
#0 37.21 Creating plot data: parents_lineage
#0 37.21 Creating plot data: cluster_id
#0 37.21 Creating plot data: rbd_level
#0 37.21 Traceback (most recent call last):
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6587, in insert
#0 37.21     item = self._validate_fill_value(item)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/numeric.py", line 425, in _validate_fill_value
#0 37.21     super()._validate_fill_value(value)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 4942, in _validate_fill_value
#0 37.21     raise TypeError
#0 37.21 TypeError
#0 37.21 
#0 37.21 During handling of the above exception, another exception occurred:
#0 37.21 
#0 37.21 Traceback (most recent call last):
#0 37.21   File "/ncov-recombinant/scripts/plot.py", line 607, in <module>
#0 37.21     main()
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
#0 37.21     return self.main(*args, **kwargs)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1055, in main
#0 37.21     rv = self.invoke(ctx)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
#0 37.21     return ctx.invoke(self.callback, **ctx.params)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 760, in invoke
#0 37.21     return __callback(*args, **kwargs)
#0 37.21   File "/ncov-recombinant/scripts/plot.py", line 319, in main
#0 37.21     plot_df.insert(0, "epiweek", plot_df.index)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/frame.py", line 4439, in insert
#0 37.21     self._mgr.insert(loc, column, value)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 1230, in insert
#0 37.21     new_axis = self.items.insert(loc, item)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6592, in insert
#0 37.21     dtype = self._find_common_type_compat(item)
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 5988, in _find_common_type_compat
#0 37.21     dtype = find_common_type([self.dtype, target_dtype])
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1841, in find_common_type
#0 37.21     return np.find_common_type(types, [])
#0 37.21   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/numpy/core/numerictypes.py", line 661, in find_common_type
#0 37.21     warnings.warn(
#0 37.21 DeprecationWarning: np.find_common_type is deprecated.  Please use `np.result_type` or `np.promote_types`.
#0 37.21 See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information.  (Deprecated NumPy 1.25)
#0 37.21 
#0 37.21 
#0 37.21 Removing output files of failed job plot since they might be corrupted:
#0 37.21 results/tutorial/plots
#0 37.21 Job failed, going on with independent jobs.
#0 37.21 Select jobs to execute...
#0 37.24 
#0 37.24 [Tue Jul 18 16:35:32 2023]
#0 37.24 Job 31: Plotting results.
#0 37.24 
#0 37.24   build:   tutorial
#0 37.24   log:     logs/plots_N10/tutorial_2023-07-18.log
#0 37.24   plots:   results/tutorial/plots_N10
#0 37.24   
#0 37.24 
#0 38.03 [Tue Jul 18 16:35:33 2023]
#0 38.03 Error in rule plot:
#0 38.03     jobid: 31
#0 38.03     output: results/tutorial/plots_N10
#0 38.03     log: logs/plots_N10/tutorial_2023-07-18.log (check log file(s) for error message)
#0 38.03     shell:
#0 38.03         
#0 38.03     python3 scripts/plot.py       --input results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_N10       --lag 4       --geo country       --weeks 16       --min-date 2022-02-09       --max-date 2022-07-04       --min-cluster-size 10       > logs/plots_N10/tutorial_2023-07-18.log 2>&1;
#0 38.03 
#0 38.03     # Extract the cluster IDs to be plotted
#0 38.03     cluster_ids=$(csvtk headers -t results/tutorial/plots_N10/cluster_id.tsv | tail -n+2 | tr "\n" "," | sed 's/,$/\n/g')
#0 38.03 
#0 38.03     # Plot breakpoints by clade
#0 38.03     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_N10       --parent-col parents_clade       --parent-type clade       --cluster-col cluster_id       --clusters "${cluster_ids}"              >> logs/plots_N10/tutorial_2023-07-18.log 2>&1;
#0 38.03 
#0 38.03     # Plot breakpoints by lineage
#0 38.03     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_N10       --parent-col parents_lineage       --parent-type lineage       --cluster-col cluster_id       --clusters "${cluster_ids}"              >> logs/plots_N10/tutorial_2023-07-18.log 2>&1;
#0 38.03     
#0 38.03         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
#0 38.03 Logfile logs/plots_N10/tutorial_2023-07-18.log:
#0 38.03 Importing linelist: results/tutorial/linelists/positives.tsv
#0 38.03 Filtering on data
#0 38.03 Creating pivot tables
#0 38.03 Creating plot data: lineage
#0 38.03 Creating plot data: status
#0 38.03 Creating plot data: geography
#0 38.03 Creating plot data: largest
#0 38.03 Creating plot data: designated
#0 38.03 Creating plot data: proposed
#0 38.03 Creating plot data: unpublished
#0 38.03 Creating plot data: parents_clade
#0 38.03 Creating plot data: parents_lineage
#0 38.03 Creating plot data: cluster_id
#0 38.03 Creating plot data: rbd_level
#0 38.03 Traceback (most recent call last):
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6587, in insert
#0 38.03     item = self._validate_fill_value(item)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/numeric.py", line 425, in _validate_fill_value
#0 38.03     super()._validate_fill_value(value)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 4942, in _validate_fill_value
#0 38.03     raise TypeError
#0 38.03 TypeError
#0 38.03 
#0 38.03 During handling of the above exception, another exception occurred:
#0 38.03 
#0 38.03 Traceback (most recent call last):
#0 38.03   File "/ncov-recombinant/scripts/plot.py", line 607, in <module>
#0 38.03     main()
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
#0 38.03     return self.main(*args, **kwargs)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1055, in main
#0 38.03     rv = self.invoke(ctx)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
#0 38.03     return ctx.invoke(self.callback, **ctx.params)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 760, in invoke
#0 38.03     return __callback(*args, **kwargs)
#0 38.03   File "/ncov-recombinant/scripts/plot.py", line 319, in main
#0 38.03     plot_df.insert(0, "epiweek", plot_df.index)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/frame.py", line 4439, in insert
#0 38.03     self._mgr.insert(loc, column, value)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 1230, in insert
#0 38.03     new_axis = self.items.insert(loc, item)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6592, in insert
#0 38.03     dtype = self._find_common_type_compat(item)
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 5988, in _find_common_type_compat
#0 38.03     dtype = find_common_type([self.dtype, target_dtype])
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1841, in find_common_type
#0 38.03     return np.find_common_type(types, [])
#0 38.03   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/numpy/core/numerictypes.py", line 661, in find_common_type
#0 38.03     warnings.warn(
#0 38.03 DeprecationWarning: np.find_common_type is deprecated.  Please use `np.result_type` or `np.promote_types`.
#0 38.03 See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information.  (Deprecated NumPy 1.25)
#0 38.03 
#0 38.03 
#0 38.03 Removing output files of failed job plot since they might be corrupted:
#0 38.03 results/tutorial/plots_N10
#0 38.03 Job failed, going on with independent jobs.
#0 38.03 Select jobs to execute...
#0 38.06 
#0 38.06 [Tue Jul 18 16:35:33 2023]
#0 38.06 Job 29: Plotting results.
#0 38.06 
#0 38.06   build:   tutorial
#0 38.06   log:     logs/plots_historical/tutorial_2023-07-18.log
#0 38.06   plots:   results/tutorial/plots_historical
#0 38.06   
#0 38.06 
#0 38.86 [Tue Jul 18 16:35:34 2023]
#0 38.86 Error in rule plot:
#0 38.86     jobid: 29
#0 38.86     output: results/tutorial/plots_historical
#0 38.86     log: logs/plots_historical/tutorial_2023-07-18.log (check log file(s) for error message)
#0 38.86     shell:
#0 38.86         
#0 38.86     python3 scripts/plot.py       --input results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_historical       --lag 4       --geo country                            --min-cluster-size 1       > logs/plots_historical/tutorial_2023-07-18.log 2>&1;
#0 38.86 
#0 38.86     # Extract the cluster IDs to be plotted
#0 38.86     cluster_ids=$(csvtk headers -t results/tutorial/plots_historical/cluster_id.tsv | tail -n+2 | tr "\n" "," | sed 's/,$/\n/g')
#0 38.86 
#0 38.86     # Plot breakpoints by clade
#0 38.86     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_historical       --parent-col parents_clade       --parent-type clade       --cluster-col cluster_id       --clusters "${cluster_ids}"       --autoscale       >> logs/plots_historical/tutorial_2023-07-18.log 2>&1;
#0 38.86 
#0 38.86     # Plot breakpoints by lineage
#0 38.86     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_historical       --parent-col parents_lineage       --parent-type lineage       --cluster-col cluster_id       --clusters "${cluster_ids}"       --autoscale       >> logs/plots_historical/tutorial_2023-07-18.log 2>&1;
#0 38.86     
#0 38.86         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
#0 38.86 Logfile logs/plots_historical/tutorial_2023-07-18.log:
#0 38.86 Importing linelist: results/tutorial/linelists/positives.tsv
#0 38.86 Filtering on data
#0 38.86 Creating pivot tables
#0 38.86 Creating plot data: lineage
#0 38.86 Creating plot data: status
#0 38.86 Creating plot data: geography
#0 38.86 Creating plot data: largest
#0 38.86 Creating plot data: designated
#0 38.86 Creating plot data: proposed
#0 38.86 Creating plot data: unpublished
#0 38.86 Creating plot data: parents_clade
#0 38.86 Creating plot data: parents_lineage
#0 38.86 Creating plot data: cluster_id
#0 38.86 Creating plot data: rbd_level
#0 38.86 Traceback (most recent call last):
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6587, in insert
#0 38.86     item = self._validate_fill_value(item)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/numeric.py", line 425, in _validate_fill_value
#0 38.86     super()._validate_fill_value(value)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 4942, in _validate_fill_value
#0 38.86     raise TypeError
#0 38.86 TypeError
#0 38.86 
#0 38.86 During handling of the above exception, another exception occurred:
#0 38.86 
#0 38.86 Traceback (most recent call last):
#0 38.86   File "/ncov-recombinant/scripts/plot.py", line 607, in <module>
#0 38.86     main()
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
#0 38.86     return self.main(*args, **kwargs)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1055, in main
#0 38.86     rv = self.invoke(ctx)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
#0 38.86     return ctx.invoke(self.callback, **ctx.params)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 760, in invoke
#0 38.86     return __callback(*args, **kwargs)
#0 38.86   File "/ncov-recombinant/scripts/plot.py", line 319, in main
#0 38.86     plot_df.insert(0, "epiweek", plot_df.index)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/frame.py", line 4439, in insert
#0 38.86     self._mgr.insert(loc, column, value)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 1230, in insert
#0 38.86     new_axis = self.items.insert(loc, item)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6592, in insert
#0 38.86     dtype = self._find_common_type_compat(item)
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 5988, in _find_common_type_compat
#0 38.86     dtype = find_common_type([self.dtype, target_dtype])
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1841, in find_common_type
#0 38.86     return np.find_common_type(types, [])
#0 38.86   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/numpy/core/numerictypes.py", line 661, in find_common_type
#0 38.86     warnings.warn(
#0 38.86 DeprecationWarning: np.find_common_type is deprecated.  Please use `np.result_type` or `np.promote_types`.
#0 38.86 See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information.  (Deprecated NumPy 1.25)
#0 38.86 
#0 38.86 
#0 38.86 Removing output files of failed job plot since they might be corrupted:
#0 38.86 results/tutorial/plots_historical
#0 38.86 Job failed, going on with independent jobs.
#0 38.86 Select jobs to execute...
#0 38.89 
#0 38.89 [Tue Jul 18 16:35:34 2023]
#0 38.89 Job 33: Plotting results.
#0 38.89 
#0 38.89   build:   tutorial
#0 38.89   log:     logs/plots_historical_N10/tutorial_2023-07-18.log
#0 38.89   plots:   results/tutorial/plots_historical_N10
#0 38.89   
#0 38.89 
#0 39.67 [Tue Jul 18 16:35:35 2023]
#0 39.67 Error in rule plot:
#0 39.67     jobid: 33
#0 39.67     output: results/tutorial/plots_historical_N10
#0 39.67     log: logs/plots_historical_N10/tutorial_2023-07-18.log (check log file(s) for error message)
#0 39.67     shell:
#0 39.67         
#0 39.67     python3 scripts/plot.py       --input results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_historical_N10       --lag 4       --geo country                            --min-cluster-size 10       > logs/plots_historical_N10/tutorial_2023-07-18.log 2>&1;
#0 39.67 
#0 39.67     # Extract the cluster IDs to be plotted
#0 39.67     cluster_ids=$(csvtk headers -t results/tutorial/plots_historical_N10/cluster_id.tsv | tail -n+2 | tr "\n" "," | sed 's/,$/\n/g')
#0 39.67 
#0 39.67     # Plot breakpoints by clade
#0 39.67     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_historical_N10       --parent-col parents_clade       --parent-type clade       --cluster-col cluster_id       --clusters "${cluster_ids}"       --autoscale       >> logs/plots_historical_N10/tutorial_2023-07-18.log 2>&1;
#0 39.67 
#0 39.67     # Plot breakpoints by lineage
#0 39.67     python3 scripts/plot_breakpoints.py       --lineages results/tutorial/linelists/lineages.tsv       --lineage-col recombinant_lineage_curated       --positives results/tutorial/linelists/positives.tsv       --outdir results/tutorial/plots_historical_N10       --parent-col parents_lineage       --parent-type lineage       --cluster-col cluster_id       --clusters "${cluster_ids}"       --autoscale       >> logs/plots_historical_N10/tutorial_2023-07-18.log 2>&1;
#0 39.67     
#0 39.67         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
#0 39.67 Logfile logs/plots_historical_N10/tutorial_2023-07-18.log:
#0 39.67 Importing linelist: results/tutorial/linelists/positives.tsv
#0 39.67 Filtering on data
#0 39.67 Creating pivot tables
#0 39.67 Creating plot data: lineage
#0 39.67 Creating plot data: status
#0 39.67 Creating plot data: geography
#0 39.67 Creating plot data: largest
#0 39.67 Creating plot data: designated
#0 39.67 Creating plot data: proposed
#0 39.67 Creating plot data: unpublished
#0 39.67 Creating plot data: parents_clade
#0 39.67 Creating plot data: parents_lineage
#0 39.67 Creating plot data: cluster_id
#0 39.67 Creating plot data: rbd_level
#0 39.67 Traceback (most recent call last):
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6587, in insert
#0 39.67     item = self._validate_fill_value(item)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/numeric.py", line 425, in _validate_fill_value
#0 39.67     super()._validate_fill_value(value)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 4942, in _validate_fill_value
#0 39.67     raise TypeError
#0 39.67 TypeError
#0 39.67 
#0 39.67 During handling of the above exception, another exception occurred:
#0 39.67 
#0 39.67 Traceback (most recent call last):
#0 39.67   File "/ncov-recombinant/scripts/plot.py", line 607, in <module>
#0 39.67     main()
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
#0 39.67     return self.main(*args, **kwargs)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1055, in main
#0 39.67     rv = self.invoke(ctx)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
#0 39.67     return ctx.invoke(self.callback, **ctx.params)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/click/core.py", line 760, in invoke
#0 39.67     return __callback(*args, **kwargs)
#0 39.67   File "/ncov-recombinant/scripts/plot.py", line 319, in main
#0 39.67     plot_df.insert(0, "epiweek", plot_df.index)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/frame.py", line 4439, in insert
#0 39.67     self._mgr.insert(loc, column, value)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 1230, in insert
#0 39.67     new_axis = self.items.insert(loc, item)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6592, in insert
#0 39.67     dtype = self._find_common_type_compat(item)
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 5988, in _find_common_type_compat
#0 39.67     dtype = find_common_type([self.dtype, target_dtype])
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1841, in find_common_type
#0 39.67     return np.find_common_type(types, [])
#0 39.67   File "/opt/conda/envs/ncov-recombinant-env/lib/python3.9/site-packages/numpy/core/numerictypes.py", line 661, in find_common_type
#0 39.67     warnings.warn(
#0 39.67 DeprecationWarning: np.find_common_type is deprecated.  Please use `np.result_type` or `np.promote_types`.
#0 39.67 See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information.  (Deprecated NumPy 1.25)
#0 39.67 
#0 39.67 
#0 39.67 Removing output files of failed job plot since they might be corrupted:
#0 39.67 results/tutorial/plots_historical_N10
#0 39.67 Job failed, going on with independent jobs.
#0 39.67 Select jobs to execute...
#0 39.67 
#0 39.67 [Tue Jul 18 16:35:35 2023]
#0 39.67 Job 34: Validating observed values in linelist.
#0 39.67 
#0 39.67   build:    tutorial
#0 39.67   log:      logs/validate/tutorial_2023-07-18.log
#0 39.67   expected: defaults/validation.tsv
#0 39.67   table:    results/tutorial/validate/validation.tsv
#0 39.67   
#0 39.67 
#0 40.04 [Tue Jul 18 16:35:35 2023]
#0 40.04 Finished job 34.
#0 40.04 24 of 33 steps (73%) done
#0 40.04 Exiting because a job execution failed. Look above for error message
#0 40.04 BUG: Out of jobs ready to be started, but not all files built yet. Please check https://github.com/snakemake/snakemake/issues/823 for more information.
#0 40.04 Remaining jobs:
#0 40.04  - plot: results/tutorial/plots_historical
#0 40.04  - plot: results/tutorial/plots
#0 40.04  - report: results/tutorial/report_N10/report.pptx, results/tutorial/report_N10/report.xlsx
#0 40.04  - plot: results/tutorial/plots_N10
#0 40.04  - report: results/tutorial/report_historical_N10/report.pptx, results/tutorial/report_historical_N10/report.xlsx
#0 40.04  - plot: results/tutorial/plots_historical_N10
#0 40.04  - all: 
#0 40.04  - report: results/tutorial/report_historical/report.pptx, results/tutorial/report_historical/report.xlsx
#0 40.04  - report: results/tutorial/report/report.pptx, results/tutorial/report/report.xlsx
#0 40.04 Complete log: .snakemake/log/2023-07-18T163456.314316.snakemake.log
------
Dockerfile:60
--------------------
  58 |     RUN snakemake --profile /ncov-recombinant/profiles/tutorial --dryrun
  59 |     
  60 | >>> RUN snakemake --profile /ncov-recombinant/profiles/tutorial
  61 |     
  62 |     #RUN snakemake --profile /ncov-recombinant/profiles/controls-positive
--------------------
ERROR: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh snakemake --profile /ncov-recombinant/profiles/tutorial" did not complete successfully: exit code: 1

@whottel
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whottel commented Jul 18, 2023

Thanks for looking into this.
I am good with closing this PR when rebar is realesed.

-Wes

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