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bahlolab / superSTR

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.
GNU General Public License v2.0
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help with post-processing issue #3

Closed fjmuzengyiheng closed 3 years ago

fjmuzengyiheng commented 3 years ago

Thank you for providing this outstanding repeat expansion detection tool.

I got my 4 samples(FastQ) processed, and 4 per_read.txt.gz files are ready.

The next step should be post-processing. Here is my command: _python3 /cluster/home/zengyiheng/project/zyh-pipeline/superstr/superSTR/Python/multiparse.py --input input_dir/ --output outputdir/ -@ 4 -r 150

Error occurred: Traceback (most recent call last): File "/cluster/home/zengyiheng/project/zyh-pipeline/superstr/superSTR/Python/multiparse.py", line 181, in manifest_path = os.path.abspath(args.manifest_path) File "/cluster/home/zengyiheng/.conda/envs/superstr/lib/python3.8/posixpath.py", line 374, in abspath path = os.fspath(path) TypeError: expected str, bytes or os.PathLike object, not NoneType

Could you please be so kind to help me with this problem? Thank you!

FangfeiHu commented 3 years ago

Hi @fjmuzengyiheng, I encountered the same problem with you when post-processing one sample. Did you find how to solve it?

fjmuzengyiheng commented 3 years ago

Hi @fjmuzengyiheng, I encountered the same problem with you when post-processing one sample. Did you find how to solve it?

No, I still cannot figure it out. Perhaps we can 加个微信！（Wechat: 1590599948）

FangfeiHu commented 3 years ago

Hi @fjmuzengyiheng, I encountered the same problem with you when post-processing one sample. Did you find how to solve it?

No, I still cannot figure it out. Perhaps we can 加个微信！（Wechat: 1590599948）

Sorry I didn't find your WeChat account. Could you check if the numbers are right? It seems like a phone number but lost one number.

fjmuzengyiheng commented 3 years ago

Hi @fjmuzengyiheng, I encountered the same problem with you when post-processing one sample. Did you find how to solve it?

No, I still cannot figure it out. Perhaps we can 加个微信！（Wechat: 1590599948）

Sorry I didn't find your WeChat account. Could you check if the numbers are right? It seems like a phone number but lost one number.

aaah, 15905999048 is correct!

lfearnley commented 3 years ago

Apologies for the delayed response; I'm afraid that when transferring this repository to my lab's account I dropped out of the notifications for issues.

I'll have a patch up for this shortly!

lfearnley commented 3 years ago

I've temporarily disabled running superSTR's post-processing without a manifest file.

Downstream statistical analysis (outlier detection and motif screening) requires and relies on the presence of a label telling the software what each sample is; whether it's a case, unknown or control. This label information is added during the post-processing step, so multiparse.py is complaining about the absence of a manifest.

I've updated multiparse.py and the relevant documentation for the package; again, my apologies for the delayed reply, and please let me know if there's anything else I can help you with!