Hi, I am trying to get rid of poly-a tail from my reads using
bbduk.sh, however, I got a warning like
WARNING! A KMER OPERATION WAS CHOSEN BUT NO KMERS WERE LOADED.
The commend I entered was (my reads are unpaired):
$ bbduk.sh -Xmx512m -da in=Test/WT12_4_AGTACT_R1.fastq.gz out=Test/WT12_4_C.fastq.gz literal=AAAAAA ktrim=r k=23 mink=11 hdist=1
And it returns,
BBDuk version 35.92 maskMiddle was disabled because useShortKmers=true Initial: Memory: max=514m, free=488m, used=26m Added 0 kmers; time: 0.012 seconds. Memory: max=514m, free=469m, used=45m ****** WARNING! A KMER OPERATION WAS CHOSEN BUT NO KMERS WERE LOADED. ****** ****** PLEASE ENSURE K IS LESS THAN OR EQUAL TO REF SEQUENCE LENGTHS. ****** Input is being processed as unpaired Started output streams: 0.077 seconds. Processing time: 8.404 seconds. Input: 1948334 reads 167556724 bases. KTrimmed: 0 reads (0.00%) 0 bases (0.00%) Result: 1948334 reads (100.00%) 167556724 bases (100.00%) Time: 8.500 seconds. Reads Processed: 1948k 229.20k reads/sec Bases Processed: 167m 19.71m bases/sec
I checked my sequence and there was no read with less than k nucleotides. I also reduced k value and it didn't work. Could you help me out? Many thanks.