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jennahamlin / mashwrapper

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Error executing process > 'NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (1)' #7

Closed tbazilegith closed 1 year ago

tbazilegith commented 1 year ago

Description of the bug

Hi Jenna, Any ideas about what cause this error? I ran this command nextflow run mashwrapper -profile singularity --input samples_files.csv --get_database organismsheet.txt --outdir local_s2019results It started and stopped with this error: executor > local (3) [0c/0396a2] process > NFCORE_MASHWRAPPER:MASHWRAPPER:INPUT_CHECK:SAMPLESHEET_CHECK (samples_files.csv) [100%] 1 of 1 ✔ [68/81138c] process > NFCORE_MASHWRAPPER:MASHWRAPPER:ORGANISMSHEET_CHECK (organismsheet.txt) [100%] 1 of 1 ✔ executor > local (3) [0c/0396a2] process > NFCORE_MASHWRAPPER:MASHWRAPPER:INPUT_CHECK:SAMPLESHEET_CHECK (samples_files.csv) [100%] 1 of 1 ✔ [68/81138c] process > NFCORE_MASHWRAPPER:MASHWRAPPER:ORGANISMSHEET_CHECK (organismsheet.txt) [100%] 1 of 1 ✔ [40/1d7b33] process > NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:MAKE_MASH - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:MAKE_DATABASE - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:SPECIES_ID - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:COMBINED_OUTPUT - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:CUSTOM_DUMPSOFTWAREVERSIONS - Execution cancelled -- Finishing pending tasks before exit executor > local (3) [0c/0396a2] process > NFCORE_MASHWRAPPER:MASHWRAPPER:INPUT_CHECK:SAMPLESHEET_CHECK (samples_files.csv) [100%] 1 of 1 ✔ [68/81138c] process > NFCORE_MASHWRAPPER:MASHWRAPPER:ORGANISMSHEET_CHECK (organismsheet.txt) [100%] 1 of 1 ✔ [40/1d7b33] process > NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:MAKE_MASH - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:MAKE_DATABASE - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:SPECIES_ID - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:COMBINED_OUTPUT - [- ] process > NFCORE_MASHWRAPPER:MASHWRAPPER:CUSTOM_DUMPSOFTWAREVERSIONS - Execution cancelled -- Finishing pending tasks before exit -[jennahamlin/mashwrapper] Pipeline completed with errors-

            Results will not be emailed. 
            Please check your specified out directory for the results. 
            Your results folder is called: local_s2019results

WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info. Error executing process > 'NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (1)'

Caused by: Missing output file(s) *.fna expected by process NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (1)

Command executed: Thanks!

Command used and terminal output

No response

Relevant files

No response

System information

No response

jennahamlin commented 1 year ago

@tbazilegith

Were you able to successfully run the test dataset for getting genomes and running the test (testGet)? nextflow run mashwrapper -profile testGet,YOURPROFILE

Additionally, when I run the tool I have to include a configuration file to specify certificates which is located here: https://github.com/jennahamlin/mashwrapper/blob/main/conf/nfcore_custom.config

My command looks like this: nextflow run mashwrapper -profile testGet,singularity --custom_config_base /scicomp/home-pure/ptx4/mashwrapper/conf

Though you would need to change the path to the configuration file to whatever is specific for you.

tbazilegith commented 1 year ago

Hi Jenna, Thanks for the reply! The tool ran successfully with testUse (nextflow run mashwrapper -profile testUse,singularity ), but didn't with testGet. below is the command I used nextflow run mashwrapper -profile testGet,singularity --custom_config_base mashwrapper/conf (my working dir is parent to mashwrapper/) 1st I got this WARNING: Could not load nf-core/config profiles: mashwrapper/conf/nfcore_custom.config 2nd, here is the error (sorry it's long)

WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info. Error executing process > 'NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (5)'

Caused by: Process NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES (5) terminated with an error exit status (1)

Command executed:

Original downloadGenome.sh script allows user to specify using conda

environment, incorporate a boolean for conda to be used with -c flag

export nf variable to tell downloadGenome script if nextflow is in use

nf="This is script is running via NextFlow" export nf

if [[ "false" != false ]]; then /blue/bphl-florida/t.bazile1/aphl_bi_fellow/data/legionella/mashwrapper_dir/mashwrapper/bin/downloadGenome.sh -c "false" -s "legionella oakridgensis" -a "false" else /blue/bphl-florida/t.bazile1/aphl_bi_fellow/data/legionella/mashwrapper_dir/mashwrapper/bin/downloadGenome.sh -c "false" -s "legionella oakridgensis" fi

cat <<-END_VERSIONS > versions.yml "NFCORE_MASHWRAPPER:MASHWRAPPER:DOWNLOAD_GENOMES": datasets: $(datasets version | sed 's/Datasets //g') dataformat: $(dataformat version | sed 's/Dataformat //g') END_VERSIONS

Command exit status: 1

Command output: Confirming both NCBI datasets/dataformat tools and Mash are available...

Command error: Confirming both NCBI datasets/dataformat tools and Mash are available... NCBI dataformat is not installed. Exiting.

Thanks, TJ

jennahamlin commented 1 year ago

Hi TJ-

For the test dataset and to use the custom config file, you must specify the full path to the file but not the file name, so this would not work: --custom_config_base mashwrapper/conf while this works for me: --custom_config_base /scicomp/home-pure/ptx4/mashwrapper/conf and this is what I get when I am in conf folder within mashwrapper and I pwd

tbazilegith commented 1 year ago

Hi Jenna, Thank you so much! It worked. -[jennahamlin/mashwrapper] Pipeline completed successfully-

So, does that suggest I have to provide the full path of the custom config - when I use my own data?

tbazilegith commented 1 year ago

It works well. Thanks!

jennahamlin commented 1 year ago

@tbazilegith glad you were able to get it working:)