Error Summary #96

josefdiaz · 2023-07-19T11:02:35Z

Hi Felipe,
Could you help with this issue I've got when running bacannot everything went just fine except the pipeline arrives that step. I tried twice with differents genomes and it fails at the same point, SUMMARY.

Command line
$ nextflow run fmalmeida/bacannot --input bacannot_samplesheet.yaml --output Resultadosilvestres --bacannot_db ./bacannot_db_2023 --max_memory 100.GB -profile docker

Launching

$ nextflow run fmalmeida/bacannot     --input bacannot_samplesheet.yaml     --output Resultadosilvestres     --bacannot_db ./bacannot_db_2023   --max_memory 100.GB    -profile docker 
N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/fmalmeida/bacannot` [big_lamport] DSL2 - revision: 0798f3ce1e [master]


------------------------------------------------------
  fmalmeida/bacannot v3.2
------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : big_lamport
  containerEngine: docker
  launchDir      : /home/jfrancisco
  workDir        : /home/jfrancisco/work
  projectDir     : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot
  userName       : jfrancisco
  profile        : docker
  configFiles    : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot/nextflow.config

Input/output options
  input          : bacannot_samplesheet.yaml
  output         : Resultadosilvestres
  bacannot_db    : ./bacannot_db_2023

Max job request options
  max_memory     : 100.GB

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use fmalmeida/bacannot for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3627669

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/fmalmeida/bacannot/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (1687)
[-        ] process > BACANNOT:UNICYCLER                       -
[-        ] process > BACANNOT:FLYE                            -
[a1/448c55] process > BACANNOT:PROKKA (sample_2262)            [100%] 73 of 73 ✔
[2a/b5ccb5] process > BACANNOT:MLST (sample_2262)              [100%] 73 of 73 ✔
[27/4a09df] process > BACANNOT:BARRNAP (sample_2262)           [100%] 73 of 73 ✔
[6e/2d8836] process > BACANNOT:COMPUTE_GC (sample_2262)        [100%] 73 of 73 ✔
[70/1d73a2] process > BACANNOT:KOFAMSCAN (sample_2262)         [100%] 73 of 73 ✔
[e6/b6657d] process > BACANNOT:KEGG_DECODER (sample_2262)      [100%] 73 of 73 ✔
[08/6b5271] process > BACANNOT:PLASMIDFINDER (sample_2262)     [100%] 73 of 73 ✔
[07/496d95] process > BACANNOT:PLATON (sample_2262)            [100%] 73 of 73 ✔
[da/a90301] process > BACANNOT:ISLANDPATH (sample_2262)        [100%] 73 of 73 ✔
[f2/071924] process > BACANNOT:VFDB (sample_2262)              [100%] 73 of 73 ✔
[0e/8bc7f5] process > BACANNOT:VICTORS (sample_2262)           [100%] 73 of 73 ✔
[7e/b3f901] process > BACANNOT:PHAST (sample_2262)             [100%] 73 of 73 ✔
[85/27ae8e] process > BACANNOT:PHIGARO (sample_2262)           [100%] 73 of 73 ✔
[d7/916c42] process > BACANNOT:PHISPY (sample_2262)            [100%] 73 of 73 ✔
[41/79fa26] process > BACANNOT:ICEBERG (sample_2262)           [100%] 73 of 73 ✔
[63/004f99] process > BACANNOT:AMRFINDER (sample_2262)         [100%] 73 of 73 ✔
[02/91eff0] process > BACANNOT:CARD_RGI (sample_2262)          [100%] 73 of 73 ✔
[61/ec5110] process > BACANNOT:ARGMINER (sample_2262)          [100%] 73 of 73 ✔
[-        ] process > BACANNOT:RESFINDER                       -
executor >  local (1687)
[-        ] process > BACANNOT:UNICYCLER                       -
[-        ] process > BACANNOT:FLYE                            -
[a1/448c55] process > BACANNOT:PROKKA (sample_2262)            [100%] 73 of 73 ✔
[2a/b5ccb5] process > BACANNOT:MLST (sample_2262)              [100%] 73 of 73 ✔
[27/4a09df] process > BACANNOT:BARRNAP (sample_2262)           [100%] 73 of 73 ✔
[6e/2d8836] process > BACANNOT:COMPUTE_GC (sample_2262)        [100%] 73 of 73 ✔
[70/1d73a2] process > BACANNOT:KOFAMSCAN (sample_2262)         [100%] 73 of 73 ✔
[e6/b6657d] process > BACANNOT:KEGG_DECODER (sample_2262)      [100%] 73 of 73 ✔
[08/6b5271] process > BACANNOT:PLASMIDFINDER (sample_2262)     [100%] 73 of 73 ✔
[07/496d95] process > BACANNOT:PLATON (sample_2262)            [100%] 73 of 73 ✔
[da/a90301] process > BACANNOT:ISLANDPATH (sample_2262)        [100%] 73 of 73 ✔
[f2/071924] process > BACANNOT:VFDB (sample_2262)              [100%] 73 of 73 ✔
[0e/8bc7f5] process > BACANNOT:VICTORS (sample_2262)           [100%] 73 of 73 ✔
[7e/b3f901] process > BACANNOT:PHAST (sample_2262)             [100%] 73 of 73 ✔
[85/27ae8e] process > BACANNOT:PHIGARO (sample_2262)           [100%] 73 of 73 ✔
[d7/916c42] process > BACANNOT:PHISPY (sample_2262)            [100%] 73 of 73 ✔
[41/79fa26] process > BACANNOT:ICEBERG (sample_2262)           [100%] 73 of 73 ✔
[63/004f99] process > BACANNOT:AMRFINDER (sample_2262)         [100%] 73 of 73 ✔
[02/91eff0] process > BACANNOT:CARD_RGI (sample_2262)          [100%] 73 of 73 ✔
[61/ec5110] process > BACANNOT:ARGMINER (sample_2262)          [100%] 73 of 73 ✔
[-        ] process > BACANNOT:RESFINDER                       -
[-        ] process > BACANNOT:CALL_METHYLATION                -
[d5/04ae86] process > BACANNOT:REFSEQ_MASHER (sample_2262)     [100%] 73 of 73 ✔
[0c/ed95c8] process > BACANNOT:DIGIS (sample_2340)             [100%] 73 of 73 ✔
[42/e619d9] process > BACANNOT:ANTISMASH (sample_2262)         [100%] 73 of 73 ✔
[d5/578449] process > BACANNOT:SEQUENCESERVER (sample_2262)    [100%] 73 of 73 ✔
[89/c0fe76] process > BACANNOT:MERGE_ANNOTATIONS (sample_2262) [100%] 73 of 73 ✔
[54/ee598b] process > BACANNOT:DRAW_GIS (sample_139)           [  2%] 2 of 68
[94/c0c5ca] process > BACANNOT:GFF2GBK (sample_172)            [  4%] 3 of 68
[-        ] process > BACANNOT:CREATE_SQL                      [  0%] 0 of 68
[-        ] process > BACANNOT:JBROWSE                         -
[-        ] process > BACANNOT:REPORT                          -
[e1/96ee86] process > BACANNOT:SUMMARY (sample_160)            [  1%] 1 of 68, failed: 1
[-        ] process > BACANNOT:MERGE_SUMMARIES                 -
[4b/115153] process > BACANNOT:CIRCOS (sample_139)             [  2%] 2 of 68
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'BACANNOT:SUMMARY (sample_160)'

Caused by:
  Process `BACANNOT:SUMMARY (sample_160)` terminated with an error exit status (1)

Command executed:

  mkdir -p results/sample_160/annotation
  ln -rs annotation/* results/sample_160/annotation
  source activate falmeida-py
  falmeida-py bacannot2json -i results -o sample_160_summary.json

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/opt/conda/envs/falmeida-py/bin/falmeida-py", line 33, in <module>
      sys.exit(load_entry_point('falmeida-py==1.0.0', 'console_scripts', 'falmeida-py')())
    File "/opt/conda/envs/falmeida-py/lib/python3.7/site-packages/falmeida_py/__main__.py", line 212, in main
      bacannot2json(args['--input'], args['--output'], args['--print'])
    File "/opt/conda/envs/falmeida-py/lib/python3.7/site-packages/falmeida_py/bacannot2json.py", line 107, in bacannot2json
      plasmids_stats( bacannot_summary )
    File "/opt/conda/envs/falmeida-py/lib/python3.7/site-packages/falmeida_py/plasmid_function.py", line 73, in plasmids_stats
      bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = results['Database'].unique().item()
  ValueError: can only convert an array of size 1 to a Python scalar

Work dir:
  /home/jfrancisco/work/e1/96ee86a42df4c84ef36c2bc0c22b82

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Thanks for all.

fmalmeida · 2023-07-19T11:14:33Z

Hi @josefdiaz ,
Based on your error message, it seems that I am failing to collect the results of plasmidfinder. Maybe it is empty, or maybe it has more than one database for the given sample.

Would it be possible for you to create a tar file of this working directory and send it to me so I can fix the python script? I would suggest a command like this:

tar zcvfh error_dir_workdir.tar.gz /home/jfrancisco/work/e1/96ee86a42df4c84ef36c2bc0c22b82.

Thanks.

josefdiaz · 2023-07-19T11:49:24Z

Hi,
I send you the tar file so you can fix it when you can.
Thanks a lot.
error_dir_workdir.tar.gz

fmalmeida · 2023-07-19T12:03:38Z

Thanks. I will get back to you when I have some updates or some other questions/requests in order to solve it.

fmalmeida · 2023-07-19T12:29:09Z

Hi @josefdiaz ,

Somewhere in your output directory, or in the home directory where you launched the pipeline, you should have some nextflow report files like execution report HTML, or trace file txt file in which you can see the working directory of each task.

Can you try finding in these files, the working directory where plasmidFinder was executed for the sample_160 and send this working directory to me, or just the .command.* and log files from this task (plasmidfinder -- sample_160).

I was already able to reproduce, find and fix the issue described, however, I need to proper understand what the tool executed or generated so I know whether the fix I found is correct or not.

Thanks.

fmalmeida · 2023-07-19T12:55:33Z

Actually, this is not needed. I just checked the tools webpage, and it indeed seem to make sense. The multiple databases shown are because the gram-positive databases from the tool are split in more than one, thus the error.

I will push the changes to a new py-script version and build a new docker image that shall come for next release with new features and this bugfix.

Once the image is ready to be used (probably tomorrow), I will write here again the command you can use to try it so we can be sure it was fixed before I make the release. ( We will perform a run with only sample_160 ) since was the one that in this case triggered the error.

😉

fmalmeida · 2023-07-20T11:36:51Z

Hi @josefdiaz ,

I have pushed the docker image now trying to solve this in a new branch(new pipeline release). Can you try running this version of the pipeline on your samples with -r 96-error-summary -latest -resume? Would be something like this:

# make sure to download the latest docker image even if already having one locally
# since the code is being fixed in this image for the next version, if already locally,
# nextflow will not pull the latest

docker pull fmalmeida/bacannot:v3.3_misc

# run the pipeline with resume
nextflow run fmalmeida/bacannot \
    -r 96-error-summary \
    -latest \
    -resume \
    --input bacannot_samplesheet.yaml \
    --output Resultadosilvestres \
    --bacannot_db ./bacannot_db_2023 \
    --max_memory 100.GB \
    -profile docker

josefdiaz · 2023-07-21T08:32:08Z

Hi @josefdiaz ,

I have pushed the docker image now trying to solve this in a new branch(new pipeline release). Can you try running this version of the pipeline on your samples with -r 96-error-summary -latest -resume? Would be something like this:
# make sure to download the latest docker image even if already having one locally
# since the code is being fixed in this image for the next version, if already locally,
# nextflow will not pull the latest

docker pull fmalmeida/bacannot:v3.3_misc

# run the pipeline with resume
nextflow run fmalmeida/bacannot \
    -r 96-error-summary \
    -latest \
    -resume \
    --input bacannot_samplesheet.yaml \
    --output Resultadosilvestres \
    --bacannot_db ./bacannot_db_2023 \
    --max_memory 100.GB \
    -profile docker

Hi @fmalmeida ,
First of all, Thank you very much for all the assistance you are providing. I have executed this version of the pipeline, and it demonstrates improved performance. However, it still encounters a failure during the summary step (66 of 73). Additionally, the sample_summary.json file does not contain the Mobile Genetic Element (MGE) summary; it appears with no information, even though the different tools detect them. Below, I provide the command used to launch the pipeline and the specific error message received.
"Launching"

executor >  local (2240)
[-        ] process > BACANNOT:UNICYCLER                       -
[-        ] process > BACANNOT:FLYE                            -
[46/d8b45b] process > BACANNOT:PROKKA (sample_2340)            [100%] 73 of 73 ✔
[a2/7b2eaf] process > BACANNOT:MLST (sample_2340)              [100%] 73 of 73 ✔
[a1/89c372] process > BACANNOT:BARRNAP (sample_2340)           [100%] 73 of 73 ✔
[f5/a3a95c] process > BACANNOT:COMPUTE_GC (sample_2340)        [100%] 73 of 73 ✔
[71/ef2d53] process > BACANNOT:KOFAMSCAN (sample_2340)         [100%] 73 of 73 ✔
[fa/e473bc] process > BACANNOT:KEGG_DECODER (sample_2340)      [100%] 73 of 73 ✔
[73/5303af] process > BACANNOT:PLASMIDFINDER (sample_2340)     [100%] 73 of 73 ✔
[41/befa01] process > BACANNOT:PLATON (sample_2340)            [100%] 73 of 73 ✔
[7d/6d3087] process > BACANNOT:MOBSUITE (sample_2340)          [100%] 73 of 73 ✔
[78/f06a12] process > BACANNOT:ISLANDPATH (sample_2340)        [100%] 73 of 73 ✔
[76/d605b3] process > BACANNOT:INTEGRON_FINDER (sample_2340)   [100%] 73 of 73 ✔
[-        ] process > BACANNOT:INTEGRON_FINDER_2GFF            -
[fa/fcd77c] process > BACANNOT:VFDB (sample_2340)              [100%] 73 of 73 ✔
[9f/11b75a] process > BACANNOT:VICTORS (sample_2340)           [100%] 73 of 73 ✔
[5f/861335] process > BACANNOT:PHAST (sample_2340)             [100%] 73 of 73 ✔
[20/3e3576] process > BACANNOT:PHIGARO (sample_2340)           [100%] 73 of 73 ✔
[cf/6f7c80] process > BACANNOT:PHISPY (sample_2340)            [100%] 73 of 73 ✔
[32/19f100] process > BACANNOT:ICEBERG (sample_2340)           [100%] 73 of 73 ✔
[b9/70bfc1] process > BACANNOT:AMRFINDER (sample_2340)         [100%] 73 of 73 ✔
[0b/159fd0] process > BACANNOT:CARD_RGI (sample_2340)          [100%] 73 of 73 ✔
[e1/aa2279] process > BACANNOT:ARGMINER (sample_2340)          [100%] 73 of 73 ✔
[-        ] process > BACANNOT:RESFINDER                       -
[-        ] process > BACANNOT:CALL_METHYLATION                -
[b3/94b31a] process > BACANNOT:REFSEQ_MASHER (sample_2340)     [100%] 73 of 73 ✔
[dc/5fd44a] process > BACANNOT:DIGIS (sample_2231)             [100%] 73 of 73 ✔
[ca/f2e764] process > BACANNOT:ANTISMASH (sample_2340)         [100%] 73 of 73 ✔
[29/c22dc4] process > BACANNOT:SEQUENCESERVER (sample_2340)    [100%] 73 of 73 ✔
[ff/30466a] process > BACANNOT:MERGE_ANNOTATIONS (sample_2340) [100%] 73 of 73 ✔
[ee/4eda6f] process > BACANNOT:DRAW_GIS (sample_2340)          [100%] 73 of 73 ✔
[17/7de969] process > BACANNOT:GFF2GBK (sample_320)            [100%] 73 of 73 ✔
[aa/dc59c5] process > BACANNOT:CREATE_SQL (sample_2340)        [100%] 73 of 73 ✔
[a9/2352f8] process > BACANNOT:JBROWSE (sample_356)            [ 78%] 57 of 73
[-        ] process > BACANNOT:REPORT                          [  0%] 0 of 73
[a0/cc6cf8] process > BACANNOT:SUMMARY (sample_2204)           [ 90%] 66 of 73, failed: 1
[-        ] process > BACANNOT:MERGE_SUMMARIES                 -
[59/1d2d0e] process > BACANNOT:CIRCOS (sample_2340)            [100%] 73 of 73 ✔
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'BACANNOT:SUMMARY (sample_2114)'

Caused by:
  Process `BACANNOT:SUMMARY (sample_2114)` terminated with an error exit status (1)

Command executed:

  mkdir -p results/sample_2114/annotation
  ln -rs annotation/* results/sample_2114/annotation
  sed -i 's/s:/:/g' results/sample_2114/annotation/sample_2114.txt
  falmeida-py bacannot2json -i results -o sample_2114_summary.json

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/opt/conda/bin/falmeida-py", line 33, in <module>
      sys.exit(load_entry_point('falmeida-py==1.2.1', 'console_scripts', 'falmeida-py')())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/falmeida_py/__main__.py", line 212, in main
      bacannot2json(args['--input'], args['--output'], args['--print'])
    File "/opt/conda/lib/python3.11/site-packages/falmeida_py/bacannot2json.py", line 111, in bacannot2json
      plasmids_stats( bacannot_summary )
    File "/opt/conda/lib/python3.11/site-packages/falmeida_py/plasmid_function.py", line 28, in plasmids_stats
      results = pd.read_csv(
                ^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
      return _read(filepath_or_buffer, kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
      parser = TextFileReader(filepath_or_buffer, **kwds)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
      self._engine = self._make_engine(f, self.engine)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1679, in _make_engine
      return mapping[engine](f, **self.options)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
      self._reader = parsers.TextReader(src, **kwds)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "pandas/_libs/parsers.pyx", line 557, in pandas._libs.parsers.TextReader.__cinit__
  pandas.errors.EmptyDataError: No columns to parse from file

Work dir:
  /home/jfrancisco/work/5c/a68fe4233b293ad265ee6932bd0c42

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Files:
error_dir_workdir21.tar.gz

sample_88_summary.zip

fmalmeida · 2023-07-21T08:48:29Z

Hi @josefdiaz ,

Interesting. I will take a look at the error&data provided, and I will get back to you early next week.

Just one note for you, you can see that even though you used -resume the modules were not cached, this happened because we are now using a new branch with a new version of the code. Next time, when you run again this same branch with -resume we will see modules being cached.

Interestingly, I also saw from your message that the module INTEGRON_FINDER_2GFF was not executed when it should ... So, I will take a look at the issue so you can try it out next week and, hopefully, have it successfully.

Let's work to have it done 😄

fmalmeida · 2023-07-24T07:53:10Z

Hi @josefdiaz ,

I have updated the python-code and the docker image again to try to fix this issue.

Also, a few other things as they relate to the questions or 'blank' itens:

I tried a few other genomes and INTEGRON_FINDER_2GFF is working good, it is just not executed, when the INTEGRON_FINDER module does not produce a gbk file, meaning no integron was detected.
Currently, the MGEs dict key, only contains the integron finder resuts, since in your case, the tool did not find anything as we can see that the INTEGRON_FINDER_2GFF as not executed, the dict is empty.
Finally, I am still working on this dev branch, so that information on prophages and ICEs are added to the summary in this MGE section, however, I still did not find to do so, so they are still not there ( I am working on that ).
Then, I moved the dict key generations to the 'child-funtions' so that, if the files used to populate are not available, like the integron finder gffs, the dict key is not created, thus instead of being empty, it is not added.

Could you then try running this again, pulling the docker image once more to guarantee having the latest python-code?

# make sure to download the latest docker image even if already having one locally
# since the code is being fixed in this image for the next version, if already locally,
# nextflow will not pull the latest

docker pull fmalmeida/bacannot:v3.3_misc

# run the pipeline with resume
nextflow run fmalmeida/bacannot \
    -r 96-error-summary \
    -latest \
    -resume \
    --input bacannot_samplesheet.yaml \
    --output Resultadosilvestres \
    --bacannot_db ./bacannot_db_2023 \
    --max_memory 100.GB \
    -profile docker

Ps. Just a small note, if it works, and we manage to fix the issue, I will wrap-up what was done to do a quick bugfix patch release in the current master branch, producing v3.2.1, instead of already releasing this dev branch with v3.3. This, because, the plan for next v3.3 release with the newly added features like MOB_SUITE and INTEGRON_FINDER is planned to be released in August/September, as there are still a few things to finish as described here #88 .

So, depending on how 'early' you will need to publish or share the results of your work, maybe would worth re-analysing with the bugfix patch release v3.2.1 or even analyse again with the stable v3.3 release once released. I say this, just so you can have a stable, fixed release, so you can guarantee reproducibility 😄

josefdiaz · 2023-07-25T09:55:15Z

Hi @josefdiaz ,

I have updated the python-code and the docker image again to try to fix this issue.

Also, a few other things as they relate to the questions or 'blank' itens:

I tried a few other genomes and INTEGRON_FINDER_2GFF is working good, it is just not executed, when the INTEGRON_FINDER module does not produce a gbk file, meaning no integron was detected.

Currently, the MGEs dict key, only contains the integron finder resuts, since in your case, the tool did not find anything as we can see that the INTEGRON_FINDER_2GFF as not executed, the dict is empty.

Finally, I am still working on this dev branch, so that information on prophages and ICEs are added to the summary in this MGE section, however, I still did not find to do so, so they are still not there ( I am working on that ).

Then, I moved the dict key generations to the 'child-funtions' so that, if the files used to populate are not available, like the integron finder gffs, the dict key is not created, thus instead of being empty, it is not added.

Could you then try running this again, pulling the docker image once more to guarantee having the latest python-code?
# make sure to download the latest docker image even if already having one locally
# since the code is being fixed in this image for the next version, if already locally,
# nextflow will not pull the latest

docker pull fmalmeida/bacannot:v3.3_misc

# run the pipeline with resume
nextflow run fmalmeida/bacannot \
    -r 96-error-summary \
    -latest \
    -resume \
    --input bacannot_samplesheet.yaml \
    --output Resultadosilvestres \
    --bacannot_db ./bacannot_db_2023 \
    --max_memory 100.GB \
    -profile docker
Ps. Just a small note, if it works, and we manage to fix the issue, I will wrap-up what was done to do a quick bugfix patch release in the current master branch, producing v3.2.1, instead of already releasing this dev branch with v3.3. This, because, the plan for next v3.3 release with the newly added features like MOB_SUITE and INTEGRON_FINDER is planned to be released in August/September, as there are still a few things to finish as described here #88 .
So, depending on how 'early' you will need to publish or share the results of your work, maybe would worth re-analysing with the bugfix patch release v3.2.1 or even analyse again with the stable v3.3 release once released. I say this, just so you can have a stable, fixed release, so you can guarantee reproducibility smile

Hi @fmalmeida ,
I have tried running that again pulling the docker image and it has gone well.

# run the pipeline
nextflow run fmalmeida/bacannot \
    -r 96-error-summary \
    -latest \
    -resume \
    --input bacannot_samplesheet.yaml \
    --output Resultadosilvestres24jul \
    --bacannot_db ./bacannot_db_2023 \
    --max_memory 100.GB \
    -profile docker
N E X T F L O W  ~  version 23.04.1
Pulling fmalmeida/bacannot ...
 Fast-forward
Launching `https://github.com/fmalmeida/bacannot` [infallible_austin] DSL2 - revision: f411535503 [96-error-summary]


------------------------------------------------------
  fmalmeida/bacannot v3.3
------------------------------------------------------
Core Nextflow options
  revision         : 96-error-summary
  runName          : infallible_austin
  containerEngine  : docker
  launchDir        : /home/jfrancisco
  workDir          : /home/jfrancisco/work
  projectDir       : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot
  userName         : jfrancisco
  profile          : docker
  configFiles      : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot/nextflow.config

Input/output options
  input            : bacannot_samplesheet.yaml
  output           : Resultadosilvestres24jul
  bacannot_db      : ./bacannot_db_2023

Max job request options
  max_memory       : 100.GB

Generic options
  unicycler_version: 0.5.0--py310h6cc9453_3

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use fmalmeida/bacannot for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3627669

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/fmalmeida/bacannot/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (2337)
[-        ] process > BACANNOT:UNICYCLER                       -
[-        ] process > BACANNOT:FLYE                            -
[32/8faee8] process > BACANNOT:PROKKA (sample_2340)            [100%] 73 of 73 ✔
[e7/4d92f5] process > BACANNOT:MLST (sample_2340)              [100%] 73 of 73 ✔
[9d/88df36] process > BACANNOT:BARRNAP (sample_2340)           [100%] 73 of 73 ✔
[61/cff46e] process > BACANNOT:COMPUTE_GC (sample_2340)        [100%] 73 of 73 ✔
[23/67cd60] process > BACANNOT:KOFAMSCAN (sample_2340)         [100%] 73 of 73 ✔
[52/8a2871] process > BACANNOT:KEGG_DECODER (sample_2340)      [100%] 73 of 73 ✔
[ed/0f81eb] process > BACANNOT:PLASMIDFINDER (sample_2340)     [100%] 73 of 73 ✔
[78/ce10b1] process > BACANNOT:PLATON (sample_2340)            [100%] 73 of 73 ✔
[50/3912a7] process > BACANNOT:MOBSUITE (sample_2340)          [100%] 73 of 73 ✔
[10/f70c52] process > BACANNOT:ISLANDPATH (sample_2340)        [100%] 73 of 73 ✔
[46/7608bf] process > BACANNOT:INTEGRON_FINDER (sample_2340)   [100%] 73 of 73 ✔
[-        ] process > BACANNOT:INTEGRON_FINDER_2GFF            -
[d4/8c0439] process > BACANNOT:VFDB (sample_2340)              [100%] 73 of 73 ✔
[e9/c2f23f] process > BACANNOT:VICTORS (sample_2340)           [100%] 73 of 73 ✔
[0c/bd7efc] process > BACANNOT:PHAST (sample_2340)             [100%] 73 of 73 ✔
[e2/fc7328] process > BACANNOT:PHIGARO (sample_2340)           [100%] 73 of 73 ✔
[3b/7e7d96] process > BACANNOT:PHISPY (sample_2340)            [100%] 73 of 73 ✔
[df/207fa5] process > BACANNOT:ICEBERG (sample_2340)           [100%] 73 of 73 ✔
[87/5a54c9] process > BACANNOT:AMRFINDER (sample_2340)         [100%] 73 of 73 ✔
[1c/a3c21a] process > BACANNOT:CARD_RGI (sample_2340)          [100%] 73 of 73 ✔
[8f/8b5f4e] process > BACANNOT:ARGMINER (sample_2340)          [100%] 73 of 73 ✔
[-        ] process > BACANNOT:RESFINDER                       -
[-        ] process > BACANNOT:CALL_METHYLATION                -
[07/5af66a] process > BACANNOT:REFSEQ_MASHER (sample_2340)     [100%] 73 of 73 ✔
[17/8fb549] process > BACANNOT:DIGIS (sample_2340)             [100%] 73 of 73 ✔
[d0/246d83] process > BACANNOT:ANTISMASH (sample_2340)         [100%] 73 of 73 ✔
[4d/b3fdea] process > BACANNOT:SEQUENCESERVER (sample_2340)    [100%] 73 of 73 ✔
[cb/388b64] process > BACANNOT:MERGE_ANNOTATIONS (sample_2204) [100%] 73 of 73 ✔
[a6/cb7a55] process > BACANNOT:DRAW_GIS (sample_2204)          [100%] 73 of 73 ✔
[79/9c0d9f] process > BACANNOT:GFF2GBK (sample_320)            [100%] 73 of 73 ✔
[fe/dba607] process > BACANNOT:CREATE_SQL (sample_2204)        [100%] 73 of 73 ✔
[70/89c441] process > BACANNOT:JBROWSE (sample_2214)           [100%] 73 of 73 ✔
[d5/7d192f] process > BACANNOT:REPORT (sample_2204)            [100%] 73 of 73 ✔
[e7/2a56bf] process > BACANNOT:SUMMARY (sample_2204)           [100%] 73 of 73 ✔
[29/8039e0] process > BACANNOT:MERGE_SUMMARIES                 [100%] 1 of 1 ✔
[ae/7f9dce] process > BACANNOT:CIRCOS (sample_2204)            [100%] 73 of 73 ✔
Completed at: 24-Jul-2023 19:53:03
Duration    : 6h 5m 48s
CPU hours   : 144.3
Succeeded   : 2'337

Thanks for all your supports

fmalmeida · 2023-07-25T10:00:58Z

Hi @josefdiaz ,

Thanks for sharing. As I discussed on my last comment, I will then wrap this ticket up to create a bugfix release of the docker image on the current version, and then, I will close this ticket once this issue it is released.

Thanks for reporting it.

fmalmeida · 2023-07-26T11:01:05Z

I am closing this issue know as the docker image was just updated, meaning that the problem would not happen using the version v3.2 if using the latest docker images of the pipeline ( updated today ).

A simple docker pull fmalmeida/bacannot:v3.2_pyenv would fix v3.2 if encountering the same issue described here.

Thus, out of this ticket, two other children-issue were created:

Include known issue form #96 in the Readme #99 ( ASAP )
Update pipeline docker images from docker tags to docker shasum #100 ( for v3.3 )

fmalmeida self-assigned this Jul 19, 2023

fmalmeida added the bug Something isn't working label Jul 19, 2023

fmalmeida added this to In progress in Release v3.2.1 Jul 24, 2023

This was referenced Jul 26, 2023

Include known issue form #96 in the Readme #99

Closed

Update pipeline docker images from docker tags to docker shasum #100

Closed

fmalmeida closed this as completed Jul 26, 2023

Release v3.2.1 automation moved this from In progress to Done Jul 26, 2023

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Error Summary #96

Error Summary #96

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Error Summary #96

Error Summary #96

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josefdiaz commented Jul 19, 2023 • edited by fmalmeida

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