extract_kraken_reads with --exclude excluding multiple taxids

[Afu5956]

Hi，

I am using extract_kraken_reads.py to exclude taxid 33208 and 9606. From the output, 33208 have been excluded, but the Homo sapiens have not been excluded.

0.02	10400	0	K	33208	        Metazoa
0.02	10400	0	K1	6072	          Eumetazoa
0.02	10400	0	K2	33213	            Bilateria
0.02	10400	0	K3	33511	              Deuterostomia
0.02	10400	0	P	7711	                Chordata
0.02	10400	0	P1	89593	                  Craniata
0.02	10400	0	P2	7742	                    Vertebrata
0.02	10400	0	P3	7776	                      Gnathostomata
0.02	10400	0	P4	117570	                        Teleostomi
0.02	10400	0	P5	117571	                          Euteleostomi
0.02	10400	0	P6	8287	                            Sarcopterygii
0.02	10400	0	P7	1338369	                              Dipnotetrapodomorpha
0.02	10400	0	P8	32523	                                Tetrapoda
0.02	10400	0	P9	32524	                                  Amniota
0.02	10400	0	C	40674	                                    Mammalia
0.02	10400	0	C1	32525	                                      Theria
0.02	10400	0	C2	9347	                                        Eutheria
0.02	10400	0	C3	1437010	                                          Boreoeutheria
0.02	10400	0	C4	314146	                                            Euarchontoglires
0.02	10400	0	O	9443	                                              Primates
0.02	10400	0	O1	376913	                                                Haplorrhini
0.02	10400	0	O2	314293	                                                  Simiiformes
0.02	10400	0	O3	9526	                                                    Catarrhini
0.02	10400	0	O4	314295	                                                      Hominoidea
0.02	10400	0	F	9604	                                                        Hominidae
0.02	10400	0	F1	207598	                                                          Homininae
0.02	10400	0	G	9605	                                                            Homo
0.02	10400	10400	S	9606	                                                              Homo sapiens

The code and parameters I use:

python3 extract_kraken_reads.py -k  S1_1.clean_kneaddata_paired_12.fastq_taxid_full.krk  -s1 S1_1.clean_kneaddata_paired_1.fastq -s2 S1_1.clean_kneaddata_paired_2.fastq -o S1_1.kneaddata_paired_1_clean.fastq -o2 S1_1.kneaddata_paired_2_clean.fastq --taxid 33208 9606 --exclude --include-children -r S1_1.clean_kneaddata_paired_12.fastq_report_full.txt

Does it seem that specifying multiple ids for "--taxid" has no effect?

[Afu5956]

Sorry, I found out that it was my problem. The parameter was used wrong. "--taxids" is missing "s" in my command.