Fatal Error after running DESeq2


I am trying to run differential gene expression analysis on FeatureCounts files using DESeq2 tool but I am getting the following error:

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Tool generated the following standard error:
*Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : *

  • line 2 did not have 15 elements*
    Calls: DESeqDataSetFromHTSeqCount → lapply → lapply → FUN → read.table → scan

I also noticed that in all my FeatureCounts files the values next to the gene IDs are 0. When I check the summary table I see very high numbers of unassigned genes:

|Status|Map with BWA on data 568 and data 567 (mapped reads in BAM format)(la_d8_3)|
| — | — |
|Status|Map with BWA on data 568 and data 567 (mapped reads in BAM format)(la_d8_3)|

How can I solve this problem?

There could be mutliple things at hand here. (a) your mapping did not worked properly so please check if your reads are properly aligned and that your reads also have a decent alignment quality. (b) you might have problems with your annotation file you have used for feature counts. Check if your annotation file is in consensus with your reference which you have used for mapping. (c) feature counts is not correctly set up, e.g., the strandness is maybe incorrect. Check these things, maybe then DESeq will also work.