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relipmoc / skewer

MIT License
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Empty sequence in output file #36

Open Isoobel opened 8 years ago

Isoobel commented 8 years ago

Hello everyone,

I ran a short test on skewer and I got an empty sequence in the output file. I know this case is not supposed to happen since I tried to remove an adapter supposed to be located at the read head, but in fact it is at the tail. But maybe it would be nice remove the header too?

Here is the input file I used to test the adapters filtering:

seq1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTT seq2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTAAAA seq3 AAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAA seq4 TTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

I launched skewer with the following command line: skewer -x TTTTTTTTTTTTTTTTTTTT -1 -l 0 -k 15 -t 16 -m head input.fasta >output.fasta

Here is the output fasta file I obtained:

seq1

seq2 AAAA seq3 AAAAAAAAAAAAAAAAAAAAAAAAA seq4 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Thanks for your help!