Megan it – Tumbling Oysters

Author

Affiliation

Steven Roberts

Professor, UW - School of Aquatic and Fishery Sciences

Published

May 5, 2025

Taking Megan for a spin for Renee

Read files

ls /home/shared/16TB_HDD_01/fish546/renee/

build
F1B-KM40_merged.fastq.gz
F1B-KM40_trimmed_R1_paired.fastq.gz
F1B-KM40_trimmed_R1_unpaired.fastq.gz
F1B-KM40_trimmed_R2_paired.fastq.gz
F1B-KM40_trimmed_R2_unpaired.fastq.gz
F2R-KM41_merged.fastq.gz
F2R-KM41_trimmed_R1_paired.fastq.gz
F2R-KM41_trimmed_R1_unpaired.fastq.gz
F2R-KM41_trimmed_R2_paired.fastq.gz
F2R-KM41_trimmed_R2_unpaired.fastq.gz
fastp.html
fastp.json
md5checksums_metagenomes_2025.txt
megahit
raw-data
Trimmomatic-0.39

Diamond blast

    /home/shared/diamond-2.1.8 blastx \
    --db /home/shared/16TB_HDD_01/sam/databases/blastdbs/ncbi-nr-20250429.dmnd \
    --query /home/shared/16TB_HDD_01/fish546/renee/F2R-KM41_merged.fastq.gz \
    --out ../output/sr-blastx.daa \
    --outfmt 100 \
    --top 5 \
    --block-size 15.0 \
    --index-chunks 4 \
    --threads 32

Meganizer

    /home/shared/megan-6.24.20/tools/daa-meganizer \
    --in ../output/sr-blastx.daa \
    --threads 32 \
    --mapDB ../data/megan-map-Feb2022.db

daa2rma

/home/shared/megan-6.24.20/tools/daa2rma \
--in ../output/sr-blastx.daa \
--mapDB ../data/megan-map-Feb2022.db \
--out ../output/sr-blastx-meganized.rma6 \
--threads 40 2>&1 | tee --append ../output/daa2rma_log.txt

Open MEGAN on locally and looked at rda file

pdf: http://gannet.fish.washington.edu/seashell/snaps/sr-blastx-meganized.pdf

---
title: "Megan it"
description: "taxa id from seq reads"
categories: [eDNA, fish546]
#citation: 
date: 05-05-2025
image: http://gannet.fish.washington.edu/seashell/snaps/Monosnap_sr-blastx-meganized.rma6_-_MEGAN_Community_Edition_version_6.25.10_built_27_Jun_2024_2025-05-05_13-42-33.png # finding a good image

author:
  - name: Steven Roberts
    url: 
    orcid: 0000-0001-8302-1138
    affiliation: Professor, UW - School of Aquatic and Fishery Sciences
    affiliation-url: https://robertslab.info
  #url:  # self-defined
draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready!
format:
  html:
    code-fold: FALSE
    code-tools: true
    code-copy: true
    highlight-style: github
    code-overflow: wrap
---

Taking Megan for a spin for Renee


Read files

```{bash}
ls /home/shared/16TB_HDD_01/fish546/renee/
```

```
build
F1B-KM40_merged.fastq.gz
F1B-KM40_trimmed_R1_paired.fastq.gz
F1B-KM40_trimmed_R1_unpaired.fastq.gz
F1B-KM40_trimmed_R2_paired.fastq.gz
F1B-KM40_trimmed_R2_unpaired.fastq.gz
F2R-KM41_merged.fastq.gz
F2R-KM41_trimmed_R1_paired.fastq.gz
F2R-KM41_trimmed_R1_unpaired.fastq.gz
F2R-KM41_trimmed_R2_paired.fastq.gz
F2R-KM41_trimmed_R2_unpaired.fastq.gz
fastp.html
fastp.json
md5checksums_metagenomes_2025.txt
megahit
raw-data
Trimmomatic-0.39
```

## Diamond blast

```{bash}
    /home/shared/diamond-2.1.8 blastx \
    --db /home/shared/16TB_HDD_01/sam/databases/blastdbs/ncbi-nr-20250429.dmnd \
    --query /home/shared/16TB_HDD_01/fish546/renee/F2R-KM41_merged.fastq.gz \
    --out ../output/sr-blastx.daa \
    --outfmt 100 \
    --top 5 \
    --block-size 15.0 \
    --index-chunks 4 \
    --threads 32
```

## Meganizer

```{bash}
    /home/shared/megan-6.24.20/tools/daa-meganizer \
    --in ../output/sr-blastx.daa \
    --threads 32 \
    --mapDB ../data/megan-map-Feb2022.db
```


## daa2rma


```{bash}
/home/shared/megan-6.24.20/tools/daa2rma \
--in ../output/sr-blastx.daa \
--mapDB ../data/megan-map-Feb2022.db \
--out ../output/sr-blastx-meganized.rma6 \
--threads 40 2>&1 | tee --append ../output/daa2rma_log.txt

```

Open MEGAN on locally and looked at rda file

pdf: <http://gannet.fish.washington.edu/seashell/snaps/sr-blastx-meganized.pdf>

![](http://gannet.fish.washington.edu/seashell/snaps/sr-blastx-meganized.png)