extract_kraken_reads.py No reads processed

[ireneortega]

I've just downloaded the code and run extract_kraken_reads.py this way:

./KrakenTools-master/extract_kraken_reads.py -k output.kraken -s R1.fastq -s2 R2.fastq -o R1_extracted.fastq -o2 R2_extracted.fastq -t 2 --exclude --report report.txt --fastq-output

but I got this error:

PROGRAM START TIME: 11-19-2021 08:54:26
        1 taxonomy IDs to parse
>> STEP 1: PARSING KRAKEN FILE FOR READIDS AZTI526.kraken
        0.00 million reads processed
        0 read IDs saved
>> STEP 2: READING SEQUENCE FILES AND WRITING READS
        0 read IDs found (0.00 mill reads processed)
        0 read IDs found (0.00 mill reads processed)
        0 reads printed to file
        Generated file: AZTI526_R1_extracted_kraken.fastq
        Generated file: AZTI526_R2_extracted_kraken.fastq

Why no read was processed?

[arz19893]

I got same issue , no read processed :
any suggestion?

[denise0593]

Same here. Have you solved the problem?

[hmontenegro]

Try adding -r kraken.report --include-children.

[theHatIsBack]

I've included both of those flags, and I'm still having the problem.

[gazollavolpiano]

You sure to be using the right input? For example the file [sample].kraken instead of [sample].kraken.report?