Open SusiJo opened 2 years ago
Error message when using input_type salmon:
Exiting.
Error: DESeq2.R could not find all of the specified quant.sf files!
In addition: Warning message:
In .local(x, row.names, optional, ...) : Arguments in '...' ignored
Execution halted
--> Solution: Check for typos in your samplesheet.tsv
and make sure the QBiC Codes
match the folder names of the rnaseq
output. In case of using a salmon_merged_gene_counts.tsv
, the names of the samples should be also carefully checked, as they can follow a different naming convention than the salmon folders.
Example: salmon folder name: QXXXXX:_XXX-XX
vs column name in salmon_merged_gene_counts.tsv
QXXXXX_XXX.XX
Error in deseq.R -r 2.0
Error in assay(if (opt$rlog) rld else vsd) <- limma::removeBatchEffect(assay(if (opt$rlog) rld else vsd), :
could not find function "if<-"
Execution halted
Error when running pathway_analysis.R -r 2.0.1
Error in check.length("fill") :
'gpar' element 'fill' must not be length 0
Calls: pheatmap ... rectGrob -> grob -> gpar -> validGP -> check.length
Error in deseq.R -r 2.0
Error in assay(if (opt$rlog) rld else vsd) <- limma::removeBatchEffect(assay(if (opt$rlog) rld else vsd), : could not find function "if<-" Execution halted
This is fixed on dev
Description of feature
Suggestion: Please add a troubleshooting section with common error messages that helps users to quickly understand what they're missing to get the pipeline running.
I suggest to make a collection of frequently occurring errors here where users can post their error messages and the solutions they have found.