Error in rule test_prodigal

[imonteroo]

Building DAG of jobs...
Creating conda environment envs/prodigal.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/prodigal.yaml created (location: .snakemake/conda/4edbab1558aaecb0ac56dcc0022a7d06)
Creating conda environment envs/ete3.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/ete3.yaml created (location: .snakemake/conda/504677b662d9b309a94e279cba8bc259)
Creating conda environment envs/pfam_scan.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/pfam_scan.yaml created (location: .snakemake/conda/f4814e8155a03c91d2d9cccb5c9f04af)
Creating conda environment envs/checkm.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/checkm.yaml created (location: .snakemake/conda/3711ed2a33f26ece83799275a394e167)
Creating conda environment envs/bioperl.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/bioperl.yaml created (location: .snakemake/conda/6c0f736163adb181cd1ef7fbe053b7bf)
Creating conda environment envs/phylophlan.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/phylophlan.yaml created (location: .snakemake/conda/e7a563cd3f7c0a978d8fb74f76cefc24)
Creating conda environment envs/diamond.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/diamond.yaml created (location: .snakemake/conda/75a6929f6d67262af24a40a431808705)
Creating conda environment envs/sourmash.yaml...
Downloading and installing remote packages.
Environment for /home/microviable/Programas/MAGpy/envs/sourmash.yaml created (location: .snakemake/conda/9f5d5c80ad78d231c30510ef6afd7269)
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads

---

test 1 1 1
test_checkm 1 1 1
test_checkm_plus 1 1 1
test_diamond 1 1 1
test_diamond_bin_summary_plus 1 1 1
test_diamond_report 1 1 1
test_pfam_scan 1 1 1
test_phylophlan 1 1 1
test_prodigal 1 1 1
test_sourmash 1 1 1
test_update_ete3 1 1 1
total 11 1 1

Select jobs to execute...

[Fri Apr 22 21:03:24 2022]
rule test_phylophlan:
output: test/outputs/phylophlan.txt
jobid: 10
reason: Missing output files: test/outputs/phylophlan.txt
resources: tmpdir=/tmp

	test/scripts/test_phylophlan.py test/outputs/phylophlan.txt

Activating conda environment: .snakemake/conda/e7a563cd3f7c0a978d8fb74f76cefc24
[Fri Apr 22 21:03:25 2022]
Finished job 10.
1 of 11 steps (9%) done
Select jobs to execute...

[Fri Apr 22 21:03:25 2022]
rule test_prodigal:
output: test/outputs/prodigal.txt
jobid: 8
reason: Missing output files: test/outputs/prodigal.txt
resources: tmpdir=/tmp

	test/scripts/test_prodigal.py test/outputs/prodigal.txt

Activating conda environment: .snakemake/conda/4edbab1558aaecb0ac56dcc0022a7d06
[Fri Apr 22 21:03:25 2022]
**Error in rule test_prodigal:
jobid: 8
output: test/outputs/prodigal.txt
conda-env: /home/microviable/Programas/MAGpy/.snakemake/conda/4edbab1558aaecb0ac56dcc0022a7d06
shell:

	test/scripts/test_prodigal.py test/outputs/prodigal.txt
	
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-04-22T210037.540400.snakemake.log**

[mw55309]

Sorry about the late reply

Conda behaviour changed and python was no longer installed in the prodigal environment, so the test script wouldn't run

Have updated the env and hopefully this should work fine now