Kraken unclassified

[thushandesilva]

Hi, nullarbor appears to be running OK (dependency check also passed at start), but the one issue is that the Kraken output does not appear to be working. All are unclassified. This is the Kraken aspect from the log from one of the samples. Thanks Thushan

read1="SW101A/R1.fq.gz" read2="SW101A/R2.fq.gz" outfile="SW101A/kraken.tab" cpus=4 opts="" /home/ubuntu/miniconda3/bin/../plugins/taxoner/kraken.sh /home/ubuntu/miniconda3/libexec/classify: invalid option -- 'd' Usage: classify [options] <fasta/fastq file(s)>

Options: (*mandatory)

• -H filename Kraken 2 index filename
• -t filename Kraken 2 taxonomy filename
• -o filename Kraken 2 options filename -q Quick mode -M Use memory mapping to access hash & taxonomy -T NUM Confidence score threshold (def. 0) -p NUM Number of threads (def. 1) -Q NUM Minimum quality score (FASTQ only, def. 0) -P Process pairs of reads -S Process pairs with mates in same file -R filename Print report to filename -m In comb. w/ -R, use mpa-style report -z In comb. w/ -R, report taxa w/ 0 count -n Print scientific name instead of taxid in Kraken output -C filename Filename/format to have classified sequences -U filename Filename/format to have unclassified sequences -O filename Output file for normal Kraken output

[tseemann]

My guess is you are using Conda? I think the kraken and kraken2 packages used to be broken - they both tried to install their own classify binary into the PATH. Try conda update --all to get the newer packages, or conda install --force kraken

I strongly recommend you use Kraken2 over Kraken1; it is more efficient and faster.

CC: @drpowell

[thushandesilva]

Thank you. Yes I am using conda. Let me try updating as suggested.