franciscozorrilla
commented
3 years ago Hey Sam,
It is hard to say what is going wrong since your jobs do not seem to produce log files, likely due to the --local flag. When I run metaGEM on the cluster (i.e. not using --local mode), my logs/ folder is populated with a file for each individual job, and this is where I can always see what is going wrong if my jobs fail. I'm not sure why these detailed logs dont simply get printed onto your terminal screen when running --local mode, which is what I have previously experienced. Perhaps we could force these logs to be created using some Snakemake functionalities. Could you please try modifying the following rule by adding the log parameter?
rule binRefine:
input:
concoct = f'{config["path"]["root"]}/{config["folder"]["concoct"]}/{{IDs}}/{{IDs}}.concoct-bins',
metabat = f'{config["path"]["root"]}/{config["folder"]["metabat"]}/{{IDs}}/{{IDs}}.metabat-bins',
maxbin = f'{config["path"]["root"]}/{config["folder"]["maxbin"]}/{{IDs}}/{{IDs}}.maxbin-bins'
output:
directory(f'{config["path"]["root"]}/{config["folder"]["refined"]}/{{IDs}}')
log:
"logs/binRefine.{{IDs}}.log"
benchmark:
f'{config["path"]["root"]}/{config["folder"]["benchmarks"]}/{{IDs}}.binRefine.benchmark.txt' Also make sure that the logs/ folder exists prior to running the jobs.
Regarding the failed metabat jobs, it may be possible that for your remaining 4 samples were not able to produce any bins so the job fails. You can similarly try adding the log parameter to the metabat Snakefile rule and rerun to see if you can produce logs with more info.
Please let me know if this helps. Best, Francisco
slambrechts
LiZhihua1982
Hi Francisco,
When running
bash metaGEM.sh -t binRefine --localwith the metagem env activated, I seem to get a "(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)" error for each job (both the binRefine jobs and metabatCross jobs). I can't seem to find which command is causing this though. Do you have any idea? Complete log for the first job: