kGWASflow

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Error in rule merge_kmers for the test.

7

Hi @akcorut, The errors occurred while I am testing this workflow by `kgwasflow test -t 5 --conda-frontend mamba` The error log from snakemake is ``` [Tue Dec 26 16:25:16 2023]...

LanLBio

MissingInputException in rule all

3

Hi, I'm trying to run the flow via snakemake (snakemake --cores all --use-conda ) but I get this error. https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:98: SyntaxWarning: invalid escape sequence '\ ' https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:99: SyntaxWarning: invalid escape...

Jose-LSP

Increase k-mer size above 31

3

Hi, After finding some relevant consecutive 31-mers, we would like to repeat the workflow with k=41 in order to focus our search. The template config.yaml discourages this, and it becomes...

VanOverbeeke

Error in rule kmc_canonical

7

Hello! When I run the code I get the following error and when I check the log file logs/count_kmers/kmc/22558Bue_BER03/kmc_canon.log it is empty. Any help is much appreciated! [Tue Feb 13...

spaddys

Error in rule multiqc, missing package imp

10

Hi, I'm getting an error in the multiqc step of the workflow when running it with the ecoli test dataset. Here's a snippet of the error: ``` Error in rule...

cedarwarman

Hi, I ran into an error doing the test: ``` Started analysis of individual_99_R1.fastq Failed to process file individual_99_R1.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline 'CCCFFFFFHHHHHJJJHGIJJJIJJGJGIJJJJIGIJJJIJJIFHGIIJIGJJFHEHI=DGGEEHHFFDFFFDEDEEDDBDBEFEEEEDDDDDDDDDDDDDDBDDDDDDCDDDDDDDDDDDDDADDDDDDBDDDDDDDCDDDDEDDEDEDE' didn't start with '+' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:172) at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)...

VanOverbeeke

Hello, I tested the kgwasflow with the `kgwasflow test` command. Then I got the errors below: ``` Full Traceback (most recent call last): File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snakemake/executors/__init__.py", line 2576, in run_wrapper run(...

SakaMax

Manhattan plots fail

4

Hi Kivanc, I've updated kGWASflow and tried to run the analysis including aligning the kmers. Unfortunately, generating the Manhattan plot yields errors, with unhelpful logs: ``` y_max: 19.284643066713652 y_min: 9.220349838454867...

Ax3man

Error in rule run_kmers_gwas

8

Hi @akcorut , I am running kGWASflow on a VM hosted on our server with 7TB Hard Disk and 180 G RAM. I got this message: [Thu Oct 12 01:53:07...

DavideGue

is full `snakemake` required? or would `snakemake-minimal` suffice?

2

I noticed in your `environment.yml` file you install snakemake - curious about whether you need full `snakemake` or if `snakemake-minimal` would be sufficient. The advantage is that minimal is much...

ctb