---
title: "02-SR-Megan"
format: html
editor: visual
---

Read files

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


DIamomd

```{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.meganized.daa \
    --outfmt 100 \
    --top 5 \
    --block-size 15.0 \
    --index-chunks 4 \
    --threads 32
```


```{bash}
    /home/shared/megan-6.24.20/tools/daa-meganizer \
    --in ../output/sr-blastx.meganized.daa \
    --threads 12 \
    --mapDB ../data/megan-map-Feb2022.db
```


/home/shared/megan-6.24.20/tools/daa2rma \
--in ./PSC-0519_unmapped_reads.1.blastx.meganized.daa ./PSC-0519_unmapped_reads.2.blastx.meganized.daa \
--mapDB ~/data/databases/MEGAN/megan-map-Feb2022.db \
--out ./PSC-0519_unmapped_reads.1.blastx.meganized.rma6 ./PSC-0519_unmapped_reads.2.blastx.meganized.rma6 \
--threads 40 2>&1 | tee --append daa2rma_log.txt


