Error Summary #96
Comments
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Hi @josefdiaz , 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:
Thanks. |
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Hi, |
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Thanks. I will get back to you when I have some updates or some other
questions/requests in order to solve it.
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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 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. |
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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 😉 |
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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 # 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 , 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 detailsFiles: |
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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 Interestingly, I also saw from your message that the module Let's work to have it done 😄 |
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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:
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
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Hi @fmalmeida , # 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]
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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
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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 : 2'337Thanks for all your supports |
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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. |
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I am closing this issue know as the docker image was just updated, meaning that the problem would not happen using the version A simple Thus, out of this ticket, two other children-issue were created: |
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Hi fmalmeida, Command error: Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command |
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Hi @JavariaAshraf , Thanks for sharing this one. That is a bit weird as I updated this line of code in the python package, and the current is: instead of the one in your error: Can you share your command line? I will also investigate the docker image to see if it has the latest correctly. |
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
Thanks for all.
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