search

nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Other
106 stars 27 forks source link

Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) #15

Closed suvimake closed 3 years ago

suvimake commented 4 years ago

Hi! I get the following error message with error in contrasts:

Loading counts, conditions and parameters. Loading annotation database. Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Warning message: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 'select()' returned 1:many mapping between keys and columns Filtering counts using DRIMSeq. Building model matrix. Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels Calls: model.matrix -> model.matrix.default -> contrasts<- Execution halted [Sun Jul 5 21:59:33 2020] Error in rule de_analysis: jobid: 9

I'm not sure how to fix this? I only have two biological replicates per condition (not possible to have more, unfortunately), could that raise the issue?

Also, I got an error: AttributeError in line 6 of /tools/pipeline-transcriptome-de/Snakefile: 'Workflow' object has no attribute 'overwrite_configfile' but this was solved by replacing "overwrite_configfile" with "overwrite_configfiles" in the snakefile: if not workflow.overwrite_configfiles: configfile: "config.yml"

Thanks a lot for help!

sagrudd commented 4 years ago

Hello @suvimake - I have been able to replicate this error as well and have issued a PR that appears to fix this. Please could you try again and let us know if the updated workflow works?

hqs10 commented 3 years ago

Dear @sagrudd , Dear @suvimake ,

Please could you share the ideas on how to fix that issue?

Would really appreciate your help.

sagrudd commented 3 years ago

This issue appears to be fixed and I cannot replicate the issue with the current version of the pipeline

bsipos commented 3 years ago

@suvimake Please make sure that you have the latest version of the pipeline from GitHub and that you use the --use-conda flag when you are running snakemake.