MAESTRO returns an error
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Entering edit mode
7 months ago
Luna_P • 0

Hello,

I came across MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) and wanted to use it on my data.

I have used the instructions on github and created a conda environment for MAESTRO.

Github link for MAESTRO: https://github.com/liulab-dfci/MAESTRO

However, I am encountering an error. Such as:

[Tue Jun 15 16:24:03 2021]

Error in rule scrna_analysis:

jobid: 2

output: Result/Analysis/MAESTRO_DiffGenes.tsv, Result/Analysis/MAESTRO_cluster.png, Result/Analysis/MAESTRO_annotated.png, Result/Analysis/MAESTRO.PredictedTFTop10.

shell:

python /home/k/anaconda3/envs/MAESTRO/lib/python3.8/site-packages/MAESTRO/lisa_path.py --species GRCh38 --input /home/k/sam/RAID/chr/L_M/A_P/hg38_2.1.tar.gz; Rscript /home/k/anaconda3/envs/MAESTRO/lib/python3.8/site-packages/MAESTRO/R/scRNAseq_pipe.R --expression ../QC/MAESTRO_filtered_gene_count.h5 --species GRCh38 --prefix MAESTRO --signature human.immune.CIBERSORT --outdir Result/Analysis --thread 10

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I tried updating MAESTRO, but I still got the error. I was wondering if anyone encountered similar errors and if so, what steps did you follow so that the pipeline takes place without errors?

Extra question: For annotating the cells, MAESTRO uses built-in signatures like [human.immune.CIBERSORT]. But for my data, the immune cell types won't really fit well. However, I would still like to know the list of cell types that MAESTRO is using. How can I obtain that?

Thank you! (This is my first time posting so if the format is not okay, apologies)

CIBERSORT scRNA-seq MAESTRO RNA-seq single-cell • 341 views
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1
Entering edit mode
6 months ago
Luna_P • 0

Hi again! My problem was solved with the new release of MAESTRO 1.5.0 :)

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