Cyclicgraphexception snakemake
WebDec 26, 2024 · Here the input files to the pipeline are input/x.txt and input/y.txt and these are present. According to the rule all, the target output files are a.txt and b.txt.However, when I run the pipeline, one superfluous instance of the wildcard i … WebMay 23, 2024 · snakemake -n dag tries to calculate the graph of the rules that should be executed in order to satisfy a rule named "dag" or produce a file with that name. If what you want is a graphical representation of the rules to be executed you need the --dag option, and you need to pass its output to the dot command in order to produce a picture:
Cyclicgraphexception snakemake
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Webclass CheckSumMismatchException (WorkflowError): """ "should be called to indicate that checksum of a file compared to known hash does not match, typically done with large downloads, etc. """ pass WebDec 11, 2024 · Add a rule that executes shell instead of run (just in case) Change NFS settings (sync, wdelay, atime, rsize, wsize, namlen, proto) Change automount (autofs) to mount (regular nfs) Remove isolated temporary storage ( /tmp) for Slurm jobs' Use NFS shadow directory instead of local compute nodes /tmp Completely remove shadow …
WebcyclicPath() Returns the cyclic path with the last node being the entry point of the cycle. Methods inherited from class java.lang.Throwable. addSuppressed, fillInStackTrace, … WebJun 30, 2024 · snakemake --cores all --use-conda It runs with no problems: Building DAG of jobs... Creating conda environment environment.yml... Downloading and installing remote packages. Environment for environment.yml created (location: .snakemake/conda/e0fff47f) Using shell: /usr/bin/bash Provided cores: 10 Rules claiming more threads will be scaled …
WebRaise code raise RuntimeError("Graph changed during iteration") from e if indegree_map[child] == 0: zero_indegree.append(child) del indegree_map[child] yield … WebI'm also running MetaBAT/MaxBin/DAStool via Snakemake, and I'm encountering similar errors at the MaxBin part of the pipeline - would you be willing to share your Snakemake rule(s) for creating your "{sample}_maxbin.scaffolds2bin.tsv" file? – Zoey RW. Dec 2, …
WebApr 4, 2024 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. hotels near moultonborough nhWebsnakemake / snakemake Public Notifications Fork 402 Star 1.6k Code Issues 696 Pull requests 59 Actions Projects 1 Security Insights main snakemake/snakemake/exceptions.py Go to file Cannot retrieve contributors at this time 577 lines (465 sloc) 18 KB Raw Blame hotels near moulsham street chelmsfordWebJan 9, 2024 · Graph in Python. In this graph, we can start from vertex A and reach the same vertex after traversing through the edges E 2->E 5->E 4.So, we will say that there … limestone in the bahamasWebSep 27, 2024 · 1 Answer Sorted by: 0 By issues command snakemake -np Snakefile you are asking snakemake to produce Snakefile, and it doesn't know how to do it. If your file is named Snakefile, there is no need to specify its name, if it has a different name then you can specify it using -s option. hotels near moulton northamptonWebNov 1, 2024 · edited. Running Snakemake with the --keep-going flag. Using a slightly faulty --cluster-sync submission script that returns exit code 0 even when the submitted job has been aborted and did not produce the expected output. limestone in sugar beet processingWebDec 26, 2024 · On v7.19.1+8 I get a CyclicGraphException (as below) after running snakemake -c1, which indeed seems to be your problem. >>> snakemake -c1 Building … hotels near mounds view mnWebMay 11, 2024 · Like the error message tells you, Snakemake finds a way to produce the output from two different rules: AmbiguousRuleException: Rules reorganise and get_txt_files are ambiguous for the file data/sample1/sample1_concatenated.txt. Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive. hotels near moundville al