I am using tximport to import abundance.tsv file from kalisto and I get this error:

Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13 
transcripts missing from tx2gene: 1
summarizing abundance
summarizing counts
summarizing length
Error in rowsum.default(x[sub.idx, , drop = FALSE], geneId) : 
  incorrect length for 'group'

it seems that it is reading my 13 sample tsv file but apparently only 11 of them are in the tximport object when I check the infReps

names(txi$infReps)

I have checked the folder and abundance files of the two missing samples, the look like other samples, nothing different dose anyone know what is going on?

Do you get the error on the first few samples (e.g. 1-3)?

How do you obtain the txi if there is an error? It should not be returning a txi object.

What if you run it on samples 12-13 only?