Name 'directory' is not defined
apop11 opened this issue · comments
I am trying to run metapi 1.1.0 under conda python 3.6.13. Using the "init" to init project seems to be fine. And when I try to execute statements like trimming or all, I got an error "name 'directory' is not defined" in the trimming.smk file.
alienzj on eniac ~/projects/pipelines/metapi_dev/test/issues_28 on 🌱 HEAD (63f0) 🅒 bioenv3.9
➜ snakemake --version (bioenv3.9)
7.1.1
alienzj on eniac ~/projects/pipelines/metapi_dev/test/issues_28 on 🌱 HEAD (63f0) 🅒 bioenv3.9
➜ python ../../run_metapi.py --version (bioenv3.9)
metapi version 1.1.0
alienzj on eniac ~/projects/pipelines/metapi_dev/test/issues_28 on 🌱 HEAD (63f0) 🅒 bioenv3.9
➜ python ../../run_metapi.py mag_wf rmhost_all --dry-run (bioenv3.9)
Running metapi mag_wf:
snakemake --snakefile /home/alienzj/projects/pipelines/metapi_dev/test/issues_28/../../metapi/snakefiles/mag_wf.smk --configfile ./config.yaml --cores 8 --rerun-incomplete --keep-going --printshellcmds --reason --until rmhost_all --dry-run
localrules directive specifies rules that are not present in the Snakefile:
profiling_humann3_config
dereplicate_all
profiling_humann2_config
Building DAG of jobs...
Job stats:
job count min threads max threads
----------------------- ------- ------------- -------------
prepare_short_reads 12 8 8
raw_report 12 4 4
raw_report_merge 1 4 4
rmhost_alignment_report 1 1 1
rmhost_all 1 1 1
rmhost_bowtie2 12 8 8
rmhost_report 12 4 4
rmhost_report_merge 1 4 4
trimming_fastp 12 4 4
trimming_fastp_multiqc 1 1 1
trimming_report 12 4 4
trimming_report_merge 1 4 4
total 78 1 8
Hi, I checkout the git repo to v1.1.0 tag, it means we used the same metapi.
Then I init project and dry-run rmhost_all,
I can't reproduce the same error.
Thank you very much! btw I found the problem “directory is not defined" was caused by the snakemake version, already solved it.
Thanks for your feedback.
Please let me know if you have any questions.