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Old 04-09-2018, 11:13 PM   #1
SK-N-BE
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Location: Germany

Join Date: Apr 2018
Posts: 11
Default Kraken - why not working anymore

Hello,
until recently, I was only using commercial softwares. Thus, I am new to Ubuntu and command-line tools.

I have installed kraken and last week, I was successfully running kraken. It is still running, but when I am opening the generated tab document, an "old" analysis is shown and stored in the new tab file.

Kraken seems to run as it should as indicated by the correct percentage of classified and unclassified sequences:

The old analysis that is stored in the tab has only 84% of classified sequences while the new one has 97%.

Thus, the command

kraken --db minikraken_20141208 mydata.fasta > sequences

is working:

100 sequences (5.53 Mbp) processed in 1.804s (3.3 Kseq/m, 183.84 Mbp/m).
97 sequences classified (97.00%)
3 sequences unclassified (3.00%)


But
kraken-report --db minikraken_20141208 kraken.out > mydata.tab

is not working --> here, an "old analysis" is stored in the new tab.file

What may I do so that kraken is running correctly or rather what may I do so that the new analysis is stored in the new tab document?
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Old 04-11-2018, 12:06 AM   #2
SK-N-BE
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Location: Germany

Join Date: Apr 2018
Posts: 11
Default

I found the mistake. It was a mistake in the command. The following is working:

kraken --db minikraken_20141208 mydata.fasta > sequences.kraken> kraken_mydata.out | kraken-report --db minikraken_20141208 kraken_mydata.out > mydata.tab
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