Cedar Warman

Also happening with me just as @archmageirvine describes. I will try `stageInMode` `copy`.

I tried `stageInMode copy` and it worked for me as well. Another workaround that doesn't require copying all the data is to reintroduce the GCS paths with each process that...

Does "results/reads/22558Bue_BER03/input_files.txt" have the correct file paths, are the files non-zero in size? Does the log "logs/count_kmers/kmc/22558Bue_BER03/kmc_canon.log " have any extra info in it? Sometimes it helps to load the...

Hooray! Glad it worked.

Hmm do the inputs (like `logs/count_kmers/kmc/22557Eva_AEM01/kmc_all.log` etc) have data in them? [This is where](https://github.com/akcorut/kGWASflow/blob/27654c8398249a5581c1463b2036211cb3fdbc0d/workflow/rules/count_kmers.smk#L251) the rule is calling the script that it seems like failed. If the input logs have...

Hi Kivanc, I'm getting the same error, I checked for the SAM output as you suggested and there wasn't one. All of log files in that directory were empty, except...

I've generated the SAM output, here are the first few lines: ``` @HD VN:1.5 SO:unsorted GO:query @SQ SN:SL4.0ch00 LN:9643250 @SQ SN:SL4.0ch01 LN:90863682 @SQ SN:SL4.0ch02 LN:53473368 @SQ SN:SL4.0ch03 LN:65298490 @SQ SN:SL4.0ch04...

After doing some reading, I found [this issue](https://github.com/ewels/MultiQC/issues/2112) with MultiQC. I manually installed MultiQC version 1.17 inside the Conda environment and it successfully ran. Would a fix be as simple...

Actually, I'm realizing the Dockerfile isn't actually used but rather the Conda environments are set up by snakemake-wrappers? [Here is the commit](https://github.com/snakemake/snakemake-wrappers/commit/bcd4a24f99bf6e289db22ffcadd670f91677d8d2) in the multiqc snakemake-wrappers repo where they mention...

When I was troubleshooting this I found it really helpful to manually activate the Conda environments after they were created by the pipeline and then list the installed packages to...