Test Error with make_kreport.py

[ryanwelch009]

I am receiving the following error. I am using the following command:

nextflow run /home/ryan.welch/phoenix/main.nf -profile test,singularity -entry PHOENIX --kraken2db /data/BI_data/arln/database --singularity_pull_docker_container

I am receiving the following error:
Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT (Test_Sample)'

Caused by:
Process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT (Test_Sample) terminated with an error exit status (1)

Command executed:

make_kreport.py
--input Test_Sample.kraken2_wtasmbld.classifiedreads.txt
--output Test_Sample.kraken2_wtasmbld.summary.txt
--taxonomy database_folder/ktaxonomy.tsv
--use-read-len

cat <<-END_VERSIONS > versions.yml
"PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT":
python: $(python --version | sed 's/Python //g')
krakentools: 1.2
phoenix_base_container_tag: base_v2.1.0
phoenix_base_container: sha256:f0304fe170ee359efd2073dcdb4666dddb96ea0b79441b1d2cb1ddc794de4943
END_VERSIONS

Command exit status:
1

Command output:
PROGRAM START TIME: 07-01-2024 12:56:11

STEP 1/4: Reading taxonomy database_folder/ktaxonomy.tsv...
0 nodes saved

Command error:
INFO: Converting SIF file to temporary sandbox...
Traceback (most recent call last):
File "/home/ryan.welch/phoenix/bin/make_kreport.py", line 199, in
main()
File "/home/ryan.welch/phoenix/bin/make_kreport.py", line 88, in main
t_file = open(args.tax_file,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'database_folder/ktaxonomy.tsv'
INFO: Cleaning up image...

Work dir:
/home/ryan.welch/results/work/b1/50d89b237a225dc9a39dff88de29b0

[ryanwelch009]

I could fix this error by setting my --kraken2db $PATH in my home directory. Please disregard.
RW

[jvhagey]

Hi @ryanwelch009, glad you got this fixed next time you have an issue to report, please open an issue here https://github.com/CDCgov/phoenix/issues so it can be triaged.