在使用cellranger count跑fastq文件时,会出现以下错误,“XXXX is not a pipestance directory”,应该怎么解决?? 发布于 2023-09-18 10:08・湖北 流程 蔡馥鸿 解决了吗 2024-02-21·湖南 回复喜欢 关于作者 sjdcomeon 平平无奇的读书人 回答 0 文章 1 关注者 0
如果运行cellranger发现以下报错,那就是fastq文件路径设置错误。 Martian Runtime-v4.0.11 RuntimeError: /gpfs/share/home/***/***/C240116-10XsC3 is not a pipestance directory 2024-02-28 16:25:25 Shutting down. Saving pipestance info to "C240116-10XSC3/C240116-10XSC3.mri.tgz" For assistanc...
使用Python编写脚本，实现文件的自动重命名。然后，运行cellranger count命令，对GSM3516662和GSM3516663两个样本进行定量分析。在资源有限的情况下，这种步骤简化是必要的。分析过程中，如果遇到如“~/Project/SC10X/GSM3516662 is not a pipestance directory”的错误，应检查目录结构和文件路径是否正确。分...
RuntimeError: ~/Project/SC10X/GSM3516662 is not a pipestance directory GSM3516662目录必须是由cellranger创建,也就是说,在运行cellranger之前GSM3516662目录不存在 --id 输出文件目录,每个样本一个输出目录 --sample是文件重命名哪一步的[Sample Name] 输出文件 可以参考生信技能树https://mp.weixin.qq.com/...
A large amount of information is printed on the screen as it unpacks. When it's finished, a directory containing the cellranger executable and all of its dependencies (exceptbcl2fastq) is included. The Illumina software,bcl2fastq2(version 2.20) is required forcellranger mkfastq. If you know...
RuntimeError: /home/jdoe/runs/sample345 is not a pipestance directory which indicates that you specified an--idthat corresponds to an existing directory that was not created by Cell Ranger. The following error indicates that you may already have a copy ofcellrangerrunning that is using the ...
To aggregate these datasets, you need to create a CSV containing the following columns: Column NameDescription library_idUnique identifier for this input GEM well. This will be used for labeling purposes only; it does not need to match any previous ID assigned to the GEM well. ...
The pipeline will begin to run, creating a new folder named with the aggregation ID you specified (e.g./home/jdoe/runs/AGG123) for its output. If this folder already exists,cellrangerwill assume it is an existing pipestance and attempt to resume running it. ...
RuntimeError: ~/Project/SC10X/GSM3516662 is not a pipestance directory GSM3516662目录必须是由cellranger创建,也就是说,在运行cellranger之前GSM3516662目录不存在 --id 输出文件目录,每个样本一个输出目录 --sample是文件重命名哪一步的[Sample Name] ...
//support.10xgenomics.com/foran exampleoverridefile--output-dir<PATH>Outputthe results tothisdirectory--uiport<PORT>ServewebUIat http://localhost:PORT--disable-uiDonot serve the web UI--noexitKeepwebUIrunning after pipestance completes or fails--nopreflightSkippreflight checks-h,--helpPrint...