Comments (5)
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.
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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: #510 (comment)
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
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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?
from drop.
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?
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Hi @gaynora7 , can you please try with the latest version of DROP (1.4.0)?
We updated the installRpackages script.
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Related Issues (20)
- Chunk options `#+echo` not correctly parsed HOT 1
- Incompatible with `Snakemake>=8` HOT 2
- Writing `rds` files as log can crash Snakemake execution HOT 1
- Error in h(simpleError(msg, call)) HOT 8
- requirementsR.txt referencing HEAD leads to irreproducibility / pipeline breaking HOT 3
- Problem running DROP HOT 2
- Annotation file asks for columns that shouldn't be needed HOT 2
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 10
- Pipeline fails with no significant results (AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R) HOT 1
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 2
- Pipeline FAILS when specifying subsets of genes to test HOT 1
- useNames = NA is defunct HOT 4
- conda setup using yaml doesn't work HOT 1
- QUESTION: specifying samples for sampleExclusionMask in OUTRIDER HOT 2
- No Overview.html file after aberrantSplicing analysis with DROP v1.4.0 HOT 4
- Can't load fds-object from DROP in R HOT 2
- Results doubts HOT 2
- Error in checkForAndCreateDir HOT 5
- Safe way to rerun crashed pipeline HOT 8
- Error in rule AberrantExpression_pipeline_OUTRIDER_Summary_R HOT 1
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