# Bowtie2 removed the entire reads from my fecal metagenomic data

**URL:** https://forum.biobakery.org/t/bowtie2-removed-the-entire-reads-from-my-fecal-metagenomic-data/7345
**Category:** KneadData
**Created:** [August 9, 2024, 1:16pm UTC](https://forum.biobakery.org/t/bowtie2-removed-the-entire-reads-from-my-fecal-metagenomic-data/7345 "2024-08-09T13:16:55Z")
**Posts on this page:** 1
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<div class="post-metadata">

### Author: ![marvin](https://avatars.discourse-cdn.com/v4/letter/m/2bfe46/32.png) [@marvin](https://forum.biobakery.org/u/marvin)
#### Post date: [August 9, 2024, 2:30pm UTC](https://forum.biobakery.org/t/bowtie2-removed-the-entire-reads-from-my-fecal-metagenomic-data/7345/2 "2024-08-09T14:30:57Z")

</div>

I found a similar post [here](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/10). 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`

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

```

`zcat Sample_R2.fq.gz | head -4`

```auto
@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](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/31).

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