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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
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CalledProcessError in installRPackages.R #528

Open gaynora7 opened 5 months ago

gaynora7 commented 5 months ago

Hi Gagneur Lab,

I'm having some issues recently when executing DROP (snakemake aberrantSplicing in this case). I keep getting the following error:

WARNING: 7 files missing in samples annotation. Ignoring... /vcu_gpfs2/home/gaynora/DROP/udx_1015/Output/processed_data/aberrant_expression/params/config/AberrantExpression_config.tsv Param Files do not match. Updating to current Sample Annotation

/vcu_gpfs2/home/gaynora/DROP/udx_1015/Output/processed_data/aberrant_splicing/params/config/AberrantSplicing_config.tsv Param Files do not match. Updating to current Sample Annotation

check for missing R packages CalledProcessError in file /vcu_gpfs2/home/gaynora/DROP/udx_1015/Snakefile, line 13: Command '['Rscript', PosixPath('/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/installRPackages.R'), PosixPath('/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/requirementsR.txt')]' returned non-zero exit status 1. File "/vcu_gpfs2/home/gaynora/DROP/udx_1015/Snakefile", line 13, in <module> File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/setupDrop.py", line 35, in installRPackages File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 448, in check_returncode

Not sure how to fix this error, could someone please provide some suggestions?

Thanks!

Python version 3.8.17 Conda version 23.3.17 Drop version 1.3.3 R version 4.3.1

vyepez88 commented 5 months ago

Hi, not sure, did the demo run through? Also, it seems that 7 (either RNA-seq BAM or DNA VCF) files mentioned in your sample annotation do not exist.

gaynora7 commented 5 months ago

Demo ran fine! No issues there

Yes, I updated my sample annotation file to fix the "files missing in sample annotation" error. I still get the same error involving requirementsR.txt I gave in the original post.

I think it is related to this post: https://github.com/gagneurlab/drop/issues/510#issue-2096958892

Someone proposed an ammendment to the installRPackages.R script. I tried changing the script with the proposed fix, but then I got this error:

check for missing R packages OSError in file /vcu_gpfs2/home/gaynora/DROP/udx_1015/Snakefile, line 13: [Errno 8] Exec format error: PosixPath('/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/installRPackages.R') File "/vcu_gpfs2/home/gaynora/DROP/udx_1015/Snakefile", line 13, in File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/setupDrop.py", line 40, in installRPackages File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 493, in run File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 858, in init File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 1720, in _execute_child

AtaJadidAhari commented 5 months ago

Hi, can you please share your config file? it seems like it passes the requirements.txt installation part and gets an error in packages related to your config at line 40 of setupDrop.py:

39: pkg_assembly_name = config.genome.getBSGenomeName() 40: response = subprocess.run(["Rscript", script, pkg_assembly_name], stderr=subprocess.STDOUT)

where it tries to install BSgenome based on your genome version, which I would assume it's hg38 since the demo ran through for you. Can you please install this package before running the pipeline using BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") in your environment and rerun the pipeline?

gaynora7 commented 5 months ago

Hi, Attached is my config file! I installed BSgenome.Hsapiens.UCSC.hg38 in the environment, but I am still getting the same error.

Also of note- I get this error in my output file when I execute the snakemake job: Error: unexpected ',' in: " if (!pckg_name %in% installed$Package || (!is.na(version) && compareVersion(installed[Package == pckg_name, Version])," Execution halted

Perhaps something is wrong with the syntax in the installRPackages.R script?

config_file.txt

vyepez88 commented 3 months ago

Hi @gaynora7 , can you please try with the latest version of DROP (1.4.0)? We updated the installRpackages script.