krakenuniq-extract-reads error

[km-2021]

I tried to extract reads with TID 3014784 using krakenuniq-extract-reads from KrakenUniq. According to the kraken uniq report, there are 1000 reads for 3014784, but 0 reads were extracted.

[BhawnaY16]

I am trying the same.Read count is zero.Can someone please help

[salzberg]

There's not enough information here for us to tell what went wrong. krakenuniq-extract-reads needs the taxonomy ID, the raw kraken output file (one line per read), and the fastq file, and it's a simple matter to extract the reads with those inputs. I'm guessing someone is wrong with one of your files, or you're giving it the "report" file instead of the raw output file.

[jenniferlu717]

@km-2021 @BhawnaY16 we will need the report, and an example of the read IDs and an example of the kraken output file.

Please provide

1. the full kraken report
2. the command line being run
3. at least the first 10 lines of your FASTA or FASTQ file
4. at least the first 10 lines of the kraken output file

You can email all of this to jlu26@jhmi.edu and I will take a look