no reads generated after running extract_kraken_reads.py

[caizhangbin]

Hi there, I am trying to use extract_kraken_reads.py to exclude the human reads.
I have kraken output file kraken.report.txt and kneaddata processed fastq file other_kneaddata.fastq as inputs:

~/KrakenTools/extract_kraken_reads.py -k kraken.report.txt -s other_kneaddata.fastq -r bac/kraken.report_2.txt -o bac/newoutput.fastq --taxid 9606 --exclude

While the program could not produce any reads:

PROGRAM START TIME: 03-28-2024 14:15:47
1 taxonomy IDs to parse

STEP 1: PARSING KRAKEN FILE FOR READIDS kraken.report.txt
0.00 million reads processed
200 read IDs saved
STEP 2: READING SEQUENCE FILES AND WRITING READS
0 read IDs found (11.76 mill reads processed)
0 read IDs found (13.48 mill reads processed)
0 reads printed to file
Generated file: bac/newoutput.fastq
PROGRAM END TIME: 03-28-2024 14:18:23

Any suggestions?

[tibitoy]

Following this question in case someone drops an answer! Running into the same issue

[qikongwanli]

Hi there, I am trying to use extract_kraken_reads.py to exclude the human reads. I have kraken output file kraken.report.txt and kneaddata processed fastq file other_kneaddata.fastq as inputs:

~/KrakenTools/extract_kraken_reads.py -k kraken.report.txt -s other_kneaddata.fastq -r bac/kraken.report_2.txt -o bac/newoutput.fastq --taxid 9606 --exclude

While the program could not produce any reads:

PROGRAM START TIME: 03-28-2024 14:15:47 1 taxonomy IDs to parse

STEP 1: PARSING KRAKEN FILE FOR READIDS kraken.report.txt
0.00 million reads processed
200 read IDs saved
STEP 2: READING SEQUENCE FILES AND WRITING READS
0 read IDs found (11.76 mill reads processed)
0 read IDs found (13.48 mill reads processed)
0 reads printed to file
Generated file: bac/newoutput.fastq
PROGRAM END TIME: 03-28-2024 14:18:23

Any suggestions?

I also face the same issue, but I solve this problem. Please just make sure that the input file of "-k " is the "--output" results of kraken2.