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mikewolfe / ChIPseq_pipeline

A general ChIP-seq pipeline to reproducibly process many samples at once.
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Not urgent: New error in quality_control #9

Closed cmhustmyer closed 3 years ago

cmhustmyer commented 3 years ago

160 of 162 steps (99%) done [INFO ] fastqc : Found 70 reports [INFO ] multiqc : Compressing plot data [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames.. [WARNING] multiqc : Use -f or --force to overwrite existing reports instead [INFO ] multiqc : Report : results/quality_control/multiqc_report_1.html [INFO ] multiqc : Data : results/quality_control/multiqc_data_1 [INFO ] multiqc : MultiQC complete Waiting at most 5 seconds for missing files. MissingOutputException in line 11 of /mnt/scratch/hustmyer/ChIPseq_pipeline/workflow/rules/quality_control.smk: Job completed successfully, but some output files are missing. Missing files after 5 seconds: results/quality_control/multiqc_report.html This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. File "/home/hustmyer@ad.wisc.edu/miniconda3/envs/ChIPseq_pipeline/lib/python3.7/site-packages/snakemake/executors/init.py", line 544, in handle_job_succes File "/home/hustmyer@ad.wisc.edu/miniconda3/envs/ChIPseq_pipeline/lib/python3.7/site-packages/snakemake/executors/init.py", line 231, in handle_job_succes Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message

Complete log: /mnt/scratch/hustmyer/ChIPseq_pipeline/.snakemake/log/2021-01-28T082431.269746.snakemake.log

I haven't gotten this error before: all of the relevant files are in the QC folder? So unsure what this is.

config - Copy.txt config.txt

mikewolfe commented 3 years ago

Weird. What are the commands you used to generate this? Did you run the pipeline, clean some stuff up, and run it again?

The multiqc error is suggesting that it has already been run and is running again: [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames..

Snakemake is looking for a multiqc_report.html file but for some reason multiqc is outputting a multiqc_report_1.html file. I'm not sure how that is occurring though. Can you walk me through the commands or series of commands that got you here?

mikewolfe commented 3 years ago

Running the pipeline multiple times without deleting the results allows multiqc to run twice and change the name of the output files. Multiqc probably shouldn't be running again when its output files already exist but closing this issue for now.