Question: (Closed) BBDuk Warning! "A KMER OPERATION WAS CHOSEN BUT NO KMERS WERE LOADED"
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gravatar for jerrywu1987
22 months ago by
jerrywu198710
jerrywu198710 wrote:

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.

rna-seq bbduk • 645 views
ADD COMMENTlink written 22 months ago by jerrywu198710

Please don't create a new question when an issue is being addressed in an existing thread.

ADD REPLYlink written 22 months ago by genomax73k

Hello jerrywu1987!

We believe that this post does not fit the main topic of this site.

Discussion happening at How to remove Poly-A tails from from QuantSeq 3' FWD data using Trimmomatic

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Do not open new threads for existing questions from another thread.

Cheers!

ADD REPLYlink modified 22 months ago • written 22 months ago by RamRS24k
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