sourmash error

[yb5339]

Hi I'm getting an error during testing whole MAGpy pipeline, in sourmash step.

Activating conda environment: /home/wikim-hpc/MAGpy/.snakemake/conda/8abd07f5f0e14ba82c88ec1b75516b52 loaded query: mags/ecoli.fa... (k=31, DNA) [Errno 2] No such file or directory: 'ecolidb.sbt.json'

Cannot open file 'ecolidb.sbt.json' [Tue May 25 16:56:05 2021] Error in rule sourmash_gather: jobid: 2 output: sourmash/ecoli.csv, sourmash/ecoli.sm conda-env: /home/wikim-hpc/MAGpy/.snakemake/conda/8abd07f5f0e14ba82c88ec1b75516b52 shell: sourmash gather -k 31 sourmash/ecoli.sig ecolidb.sbt.json -o sourmash/ecoli.csv > sourmash/ecoli.sm (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job sourmash_gather since they might be corrupted: sourmash/ecoli.csv, sourmash/ecoli.sm [Tue May 25 16:56:41 2021] Finished job 8. 4 of 13 steps (31%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/wikim-hpc/MAGpy/.snakemake/log/2021-05-25T165311.085862.snakemake.log

How can I solve this problem?

[mw55309]

Hello!

You have to edit the config.json file to point “sourmash_gbk” to a valid sourmash database….

HTH

Mick

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Hi I'm getting an error during testing whole MAGpy pipeline, in sourmash step.

Activating conda environment: /home/wikim-hpc/MAGpy/.snakemake/conda/8abd07f5f0e14ba82c88ec1b75516b52 loaded query: mags/ecoli.fa... (k=31, DNA) [Errno 2] No such file or directory: 'ecolidb.sbt.json'

Cannot open file 'ecolidb.sbt.json' [Tue May 25 16:56:05 2021] Error in rule sourmash_gather: jobid: 2 output: sourmash/ecoli.csv, sourmash/ecoli.sm conda-env: /home/wikim-hpc/MAGpy/.snakemake/conda/8abd07f5f0e14ba82c88ec1b75516b52 shell: sourmash gather -k 31 sourmash/ecoli.sig ecolidb.sbt.json -o sourmash/ecoli.csv > sourmash/ecoli.sm (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job sourmash_gather since they might be corrupted: sourmash/ecoli.csv, sourmash/ecoli.sm [Tue May 25 16:56:41 2021] Finished job 8. 4 of 13 steps (31%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/wikim-hpc/MAGpy/.snakemake/log/2021-05-25T165311.085862.snakemake.log

How can I solve this problem?

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[yb5339]

@mw55309 Thank you. I thought there was a file named 'ecolidb.sbt.json'.. anyway, it works!

[mw55309]

Hey

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

Please test it!

Cheers Mick