When I start the pipeline with the example data (from step 1), it halts at step 2. I a

Pipeline stops at step 2,about korcsmarosgroup/virallink

Comments (2)

bbazsi41 commented on August 16, 2024
Hi!
Sorry for the late answer. I'm sorry to hear that, but thank you for raising it. Can you send me the full gutcovid.out file?
Thanks,
Balazs
from virallink.
BioApple commented on August 16, 2024
Hi,
no problem. I copy my virallink.out content here, becuse I can't upload .out files

Starting differential expression analysis script: diff_expression_deseq2.R

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.16.tar.gz'
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The downloaded source packages are in
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'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'BiocVersion', 'DESeq2'
also installing the dependencies ‘fastmap’, ‘sys’, ‘bit’, ‘cachem’, ‘askpass’, ‘bitops’, ‘formatR’, ‘bit64’, ‘blob’, ‘memoise’, ‘plogr’, ‘png’, ‘Biostrings’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘colorspace’, ‘cli’, ‘crayon’, ‘utf8’, ‘RCurl’, ‘GenomeInfoDbData’, ‘zlibbioc’, ‘matrixStats’, ‘lambda.r’, ‘futile.options’, ‘DBI’, ‘RSQLite’, ‘KEGGREST’, ‘XML’, ‘xtable’, ‘httr’, ‘farver’, ‘labeling’, ‘lifecycle’, ‘munsell’, ‘R6’, ‘viridisLite’, ‘ellipsis’, ‘fansi’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘vctrs’, ‘GenomeInfoDb’, ‘XVector’, ‘MatrixGenerics’, ‘DelayedArray’, ‘futile.logger’, ‘snow’, ‘BH’, ‘AnnotationDbi’, ‘annotate’, ‘RColorBrewer’, ‘digest’, ‘glue’, ‘gtable’, ‘isoband’, ‘rlang’, ‘scales’, ‘tibble’, ‘withr’, ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘Biobase’, ‘BiocParallel’, ‘genefilter’, ‘locfit’, ‘geneplotter’, ‘ggplot2’, ‘Rcpp’, ‘RcppArmadillo’

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The downloaded source packages are in
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── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
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── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
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Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
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Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
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estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

Starting Omnipath/Dorothea download script: Downloading_omnipath_dorothea.R

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Loading required package: devtools
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── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
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[2021-11-21 14:14:17] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2021-11-21 14:14:19] [SUCCESS] [OmnipathR] Downloaded 8344 interactions.
[2021-11-21 14:14:26] [SUCCESS] [OmnipathR] Downloaded 42498 interactions.
[2021-11-21 14:14:32] [SUCCESS] [OmnipathR] Downloaded 22300 interactions.
[2021-11-21 14:14:33] [WARN]    [OmnipathR] Unknown parameter: `confidence_level`.
[2021-11-21 14:14:34] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
Error in ia_transcriptional$consensus_stimulation + ia_transcriptional$consensus_inhibition : 
  non-numeric argument to binary operator
Calls: [ -> [.tbl_df
Execution halted
from virallink.
Pipeline stops at step 2 about virallink HOT 2 OPEN

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