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fw262 / TAR-scRNA-seq

scRNA-seq analysis beyond gene annotations using transcriptionally active regions (TARs) generated from sequence alignment data
GNU General Public License v3.0
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Error in rule MergeBamAlignment #13

Open HUPINLI opened 2 years ago

HUPINLI commented 2 years ago

The following error occurred when I used the test data to run ''snakemake -R --until getMats -j [# cores]''. May I ask what might be the problem A7742%O0TALM3`2XC(RH1VU @fw262

fw262 commented 2 years ago

Hello,

Are you running the from_fastq or from_cellranger pipeline? Can you check you have the updated version of Picard tools version 2.18.29-0 or greater?

Best, Michael

HUPINLI commented 2 years ago

Hello,

Thank you for your reply.I am running the from_fastq,and my picard tools version is 2.26.10.

thanks, Pinli Hu

HUPINLI commented 2 years ago

Hello, And there is the log file,please check it: snakemakeLog.txt

thanks, Pinli Hu

HUPINLI commented 2 years ago

Hello,

It looks like there are two types of errors that can occur simultaneously or separately as I change the parameters(-j [# cores]).

thanks, Pinli Hu

fw262 commented 2 years ago

Hello,

It seems like you're getting the error at the gtfToGenePred step. Can you make sure you are running the latest version of this tool? Link here https://bioconda.github.io/recipes/ucsc-gtftogenepred/README.html.

If that doesn't work, try the fix shared in this post https://askubuntu.com/questions/339364/libssl-so-10-cannot-open-shared-object-file-no-such-file-or-directory.

Best, Michael

HUPINLI commented 2 years ago

Hello,

Actually, I've already solved those problems,thank you very much for your help.However,when I ran R script which is contained in rule getDiffMarkers,the following error occurred.I wander why.Could you please help me?'

EISR~P{TE_H$6YSJ2`8N}W7

thanks, Pinli Hu

fw262 commented 2 years ago

Hi Pinli,

That error may be related to the seurat version that you are using. Try changing markersUTAR$avg_logFC to markersUTAR$avg_log2FC in analyzeExpressionMat.R.

It is also possible that there is simply no differentially expressed uTARs in your dataset. If you are familiar with R, you can run the code in analyzeExpressionMat.R up to allMarkers <- FindAllMarkers(sample_combined, only.pos = T, min.pct = 0.25, logfc.threshold = 0.25) and see the result in allMarkers. You may need to adjust the min.pct and logfc.threshold values to pick up differentially expressed UTARs.

Best, Micahel

HUPINLI commented 2 years ago

Hi Micahel，

I have solved the problem by following your advice(changing markersUTAR$avg_logFC to markersUTAR$avg_log2FC), thank you~

thanks, Pinli Hu