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hxj5 / xcltk

Toolkit for XClone preprocessing to detect CNVs from scRNA-seq data
Apache License 2.0
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xcltk baf - AssertionError #10

Closed stublakemore closed 1 week ago

stublakemore commented 1 week ago

Dear Xianjie,

Thanks for the amazing package! However, I'm running into an issue when running xcltlk baf, where an AssertionError occurs:

xcltk baf AssertionError.pdf

It would be great if you can point me in the right direction what's going wrong... I'm running xcltk in a conda environment on a MacBook Pro, and running it using files on a server (not sure whether this might somehow be causing the issue?).

Many thanks,

Stuart

hxj5 commented 1 week ago

Hi Stuart, thanks for the detailed feedback. According to the log file, it seems some phased VCF files are missing, possibly due to failing to access the net-file on server or errors in reference phasing with Eagle2.

Can you check whether the phased VCF files (with suffix .phased.vcf.gz) for all autosome chromosomes, e.g., chr1 to 22 if human genome, are present in the phasing folder? If some phased files are indeed missing, can you share the corresponding log file in scripts/phasing/ folder? Thanks!

stublakemore commented 1 week ago

Dear Xianjie,

Thank you for your quick response! Unfortunately I don't have any .phased.vcf.gz files, but I do have .vcf.gz and vcf.gz.csi files for chr1-22, which are all in the phasing folder. So I guess based on what you were expecting they're all missing? Here the zipped scripts/phasing/ folder as requested.

Cheers,

Stuart

phasing.zip

hxj5 commented 1 week ago

Hi, as you can see from every log file of the phasing step, e.g., the phasing/phasing_1.log, the eagle tool can not be executed. You may need to check whether the eagle binary file can be accessed and has proper permission settings, especially the execute permission "x".

Sample_6_baf/scripts/phasing/run_phasing_1.sh: line 2: /Volumes/AG_Pallasch/Verzeichnis_1/CENETM_Lab/SFB_1530_B02/CITE_Seq/CLL_PBMCs_1_TX231/Eagle_v2.4.1/eagle: cannot execute binary file
stublakemore commented 1 week ago

Dear Xianjie,

After reading into the eagle release information, I found out it was only ever optimised for linux. Although unix on Mac OS is a very similar operating system to linux, I couldn't figure out how to fix the AssertionError issue in unix. However, installing xcltk exactly as you described on our high performance computer (which is a linux system) solved the issue. For future readers of this issue that are also Mac OS users without access to a HPC, I would recommend installing a virtual box (for example here: https://macpaw.com/how-to/install-linux-on-mac).

Many thanks for your support,

Stuart