mw55309
commented
1 year ago 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
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
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
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:
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**