error: sequence with ID `GWNJ-7/1' is empty

[Nayeli Gutiérrez]

Dear ABySS community,

Could you suggest a workaround to this error?

error: sequence with ID `GWNJ-1012:59:GW200317505th:4:1101:10682:1047/1' is empty

make: *** [Tdiscoideus1-1.fa] Error 1

I trimmed the fasta files with cutadapt but kept having the error.

Any help would be appreciated,

Nayeli

[Lauren Coombe]

Hi Nayeli,

Have you taken a look at that sequence? Is it in fact empty?

You should make sure that any sequences that are empty (due to trimming) and their pair are removed from your input reads file. It's important to remove any reads along with their pair to retain the correct paired-end formatting of your reads file. The "seqtk" tools are quite useful for those operations -- filtering sequences based on their length, and dropping any unpaired reads from an interleaved file (seqtk dropse).

Hope that helps and thank you for your interest in ABySS,

Lauren