Closed alexmascension closed 10 months ago
Hi! Any news on this? Thanks!
Sorry for the slow response, it's been a complicated summer for me.
First thing to say is that we have not optimised this workflow for use with small RNAs, and other people have had similar issues, related I believe to the sparsity of these matrices. The error message here is probably bang-on, in that the internal filtering that happens here is excluding all your rows due to the low counts.
You'll probably need to switch deseq2_vs_method
to rlog
to make this work at all, but I lack the small RNA experience to comment on the likely results.
Nice! I'll give it a try to see what we can do about it. Thanks!
Closing for now- feel free to reopen with any followup
Description of the bug
Hi, I'm running your pipeline after running the nfcore/smrnaseq pipeline for some miRNA detection. Currently, I'm stuck at the
NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL
step.The error reports two things:
Which I guess is some problem with saving the file, but I don't know exactly what it is. The saving path does not contain any strange characters. running with the
-profile docker,test
works also fine.The second problem may be related to
I guess this is because the counts file is short (it contains ~1300 entries/genes). However, I've tried making the
--deseq_vst_nsub
smaller (up to 10) and it still gives the same error.Command used and terminal output
Relevant files
contrasts.csv samplesheet_merged_differentialabundance.csv mature_counts_transposed.csv mmu.zip nextflow.log
System information
Nextflow version: 23.04.1.5866 Hardware: Desktop Executor: local Container engine: Docker OS: Ubuntu 22.04 Version of nf-core/smrnaseq: v2.2.1-gf7022ab Version of nf-core/differentialabundance: v1.2.0