Bowtie2 removed the entire reads from my fecal metagenomic data

Infrastructure and utilities KneadData
2

I found a similar post here. My problem is associated with the seq id.

And I checked the seq id and there’s space in my seq id.

zcat Sample_R1.fq.gz | head -4

@LH00169:221:22352TLT4:7:1101:51633:1042 1:N:0:ATGGTAAC+GTCTACCG
ANGGCTGAATAACCCGGATCTCGACGCTGCGGTTGGTGAAGATCTGGCACAGCAGCTACGTGACGAACTGGAACTGGTGAAAGGCGCGTCTAACGAGTTCGACAAAGAATTGTTCCTTGCGGGCGAAATCACTCCGGTATTCTTCGGTAC
+
I#II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

zcat Sample_R2.fq.gz | head -4

@LH00169:221:22352TLT4:7:1101:51633:1042 2:N:0:ATGGTAAC+GTCTACCG
ANATACGAAGCAGGTAAATTTGTCTTCGCTCGCTTCTACGGTACGGGTATCAGTCTGACGCGGCATCGGCGCAGGTGCCCACTCCACCAGGCCATCCAGCATATGATCGACGCCGAAGTTACCAAGCGCAGTACCGAAGAATACCGGAGT
+
I#IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII

It seems that there is a unofficial solution but I can’t understand the details.