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07_ANNOTATION

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eolesin edited this page Jun 24, 2021 · 15 revisions

Run HMMs on for single-copy core genes for each sample contig set.

for i in `cat AMOR_2020_Good`; do anvi-run-hmms -c 03_INDIV_ASSEMBLY/${i}/${i}.prefixed.contigs.db -T 50; done

Run CAT on contig sets to get taxonomic assignments of contigs

DB_PATH="/export/dahlefs/work/Databases/CAT_prepare_20210107/2021-01-07_CAT_database"
TAX_PATH="/export/dahlefs/work/Databases/CAT_prepare_20210107/2021-01-07_taxonomy"

for i in `cat AMOR_2020_Good`; 
do nice CAT contigs -c ${i}/${i}.prefixed.fa -d ${DB_PATH} \
-t ${TAX_PATH} -n 16 -o ${i}_CATout --top 11 --I_know_what_Im_doing; 
done

Gene annotation (on kjempefuru)

cd 03_INDIV_ASSEMBLY/
for SET in `cat /export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/AMOR_2020_Good`; \
    do anvi-get-sequences-for-gene-calls -c $SET/$SET.prefixed.contigs.db \
    --get-aa-sequences \ 
    -o $SET/$SET.prefixed.aminoacidseqs.fa; \
done

# using Pfams
cd ..
for i in `cat AMOR_2020_Good`; 
do anvi-run-pfams -c 03_INDIV_ASSEMBLY/${i}/${i}.prefixed.contigs.db \
--pfam-data-dir /export/dahlefs/work/Databases/2021-06-15_Pfams-DB/ -T 60; 
done

# run kegg - kofams using the dev version of Anvi'o from Achim's anvio-dev conda env.

for SET in `cat /export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/AMOR_2020_Good`; 
    do anvi-run-kegg-kofams -c 03_INDIV_ASSEMBLY/$SET/$SET.prefixed.contigs.db \
    --kegg-data-dir /export/dahlefs/work/Databases/2021-04-22_KOFAM-DB -T 40 \
    >> /export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/06_ANNOTATION/2021-05-26_anvi-run-kegg-kofams.log;
done

# Estimate metabolism

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