Error while running the test

mars188 commented 3 years ago

Hi,

I installed the MAGpy by following the described steps. But all that, when I tried running the test with the following command: snakemake --use-conda -s MAGpy

I get the following error:

Activating conda environment: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/f2a7e790 Activating conda environment: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/0a6540a5 Activating conda environment: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/3c5b4375 [Tue Nov 17 17:15:54 2020] Error in rule sourmash_sig: jobid: 3 output: sourmash/ecoli.sig conda-env: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/0a6540a5 shell: sourmash compute --scaled 1000 -k 31 -o sourmash/ecoli.sig mags/ecoli.fa (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Nov 17 17:15:54 2020] Error in rule checkm: jobid: 11 output: checkm.txt conda-env: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/f2a7e790 shell:

            checkm_db=/scratch/gencore/ma5877/MAG/checkm_data
            echo ${checkm_db} | checkm data setRoot ${checkm_db}
            checkm lineage_wf -f checkm.txt --reduced_tree -t 16 -x fa mags ./checkm

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Nov 17 17:17:25 2020] Finished job 8. 1 of 13 steps (8%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message

Please help me to fix this issue. Thanks

mars188 commented 3 years ago

Here is the complete log:

Building DAG of jobs... Creating conda environment envs/prodigal.yaml... Downloading and installing remote packages. Environment for envs/prodigal.yaml created (location: .snakemake/conda/3c5b4375) Creating conda environment envs/bioperl.yaml... Downloading and installing remote packages. Environment for envs/bioperl.yaml created (location: .snakemake/conda/0003c3c9) Creating conda environment envs/pfam_scan.yaml... Downloading and installing remote packages. Environment for envs/pfam_scan.yaml created (location: .snakemake/conda/248d4fef) Creating conda environment envs/checkm.yaml... Downloading and installing remote packages. Environment for envs/checkm.yaml created (location: .snakemake/conda/f2a7e790) Creating conda environment envs/ete3.yaml... Downloading and installing remote packages. Environment for envs/ete3.yaml created (location: .snakemake/conda/6e4bf5f9) Creating conda environment envs/diamond.yaml... Downloading and installing remote packages. Environment for envs/diamond.yaml created (location: .snakemake/conda/67f26a19) Creating conda environment envs/basic2.yaml... Downloading and installing remote packages. Environment for envs/basic2.yaml created (location: .snakemake/conda/4d1ca557) Creating conda environment envs/sourmash.yaml... Downloading and installing remote packages. Environment for envs/sourmash.yaml created (location: .snakemake/conda/0a6540a5) Using shell: /bin/bash Provided cores: 28 Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1 checkm 1 checkm_plus 1 diamond 1 diamond_bin_summary 1 diamond_bin_summary_plus 1 diamond_report 1 pfam_scan 1 phylophlan_link 1 prodigal 1 sourmash_gather 1 sourmash_report 1 sourmash_sig 13

[Tue Nov 17 17:15:52 2020] rule prodigal: input: mags/ecoli.fa output: proteins/ecoli.faa, proteins/ecoli_prodigal.gff jobid: 8 wildcards: id=ecoli

[Tue Nov 17 17:15:52 2020] rule checkm: input: mags output: checkm.txt jobid: 11 threads: 16

[Tue Nov 17 17:15:52 2020] rule sourmash_sig: input: mags/ecoli.fa output: sourmash/ecoli.sig jobid: 3 wildcards: id=ecoli

Activating conda environment: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/f2a7e790 Activating conda environment: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/0a6540a5 Activating conda environment: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/3c5b4375 /bin/bash: sourmash: command not found /bin/bash: line 1: checkm: command not found [Tue Nov 17 17:15:54 2020] Error in rule sourmash_sig: /bin/bash: line 2: checkm: command not found jobid: 3 output: sourmash/ecoli.sig conda-env: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/0a6540a5 shell: sourmash compute --scaled 1000 -k 31 -o sourmash/ecoli.sig mags/ecoli.fa (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Nov 17 17:15:54 2020] Error in rule checkm: jobid: 11 output: checkm.txt conda-env: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/conda/f2a7e790 shell:

            checkm_db=/scratch/gencore/ma5877/MAG/checkm_data
            echo ${checkm_db} | checkm data setRoot ${checkm_db}
            checkm lineage_wf -f checkm.txt --reduced_tree -t 16 -x fa mags ./checkm

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Nov 17 17:17:25 2020] Finished job 8. 1 of 13 steps (8%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /scratch/gencore/ma5877/MAG/MAGpy/.snakemake/log/2020-11-17T170653.385976.snakemake.log

mw55309 commented 3 years ago

Hey

There is a new release today that fixes a lot of sourmash and phylophlan bugs

Please test it!

Cheers Mick

WatsonLab / MAGpy

Error while running the test #25