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--- benchmarking_universal_single-copy_orthologs_busco [2024/12/10 14:47] – old revision restored (2020/04/13 08:05) 129.173.94.151
+++ benchmarking_universal_single-copy_orthologs_busco [2024/12/10 14:49] (current) – 129.173.94.151
@@ Line 81: / Line 81: @@
-* BUSCO 5.2.2 *
+** * BUSCO 5.2.2 * **
-Genomic: default metaeuk
+** Genomic: default metaeuk**
- source activate busco-5
+    source activate busco-5
- INPUT='contigs_clean.fasta'
+    INPUT='contigs_clean.fasta'
- OUTDIR='busco5_out'
+    OUTDIR='busco5_out'
- MODE='genome'
+    MODE='genome'
- # setting the lineage db
+    # setting the lineage db
- ## the latest busco db for eukaryota is odb10
+    ## the latest busco db for eukaryota is odb10
- LINEAGEDB='/scratch5/db/Eukfinder/BUSCO/busco_downloads/lineages/eukaryota_odb10/'
+    LINEAGEDB='/scratch5/db/Eukfinder/BUSCO/busco_downloads/lineages/eukaryota_odb10/'
- ## busco v5 only works with odb10
+    ## busco v5 only works with odb10
- ## it will not work with odb9
+    ## it will not work with odb9
- # run busco
+    # run busco
- ## do not specify output dir with a trailing slash, it will lead to a fatal error
+    ## do not specify output dir with a trailing slash, it will lead to a fatal error
- ## modes are genome, proteins, transcriptome
+    ## modes are genome, proteins, transcriptome
- ## the below command will use Metaeuk as gene predictor
+    ## the below command will use Metaeuk as gene predictor
- busco \
+    busco \
-     --in $INPUT \
+        --in $INPUT \
-     --out $OUTDIR \
+        --out $OUTDIR \
-     --mode $MODE \
+        --mode $MODE \
-     --lineage_dataset $LINEAGEDB \
+        --lineage_dataset $LINEAGEDB \
-     --cpu 8
+        --cpu 8
- conda deactivate
+    conda deactivate
-Proteomic:
- source activate busco-5
+** Proteomic:**
- # in the busco-5 environment, AUGUSTUS_CONFIG_PATH is set to
- # /scratch2/software/anaconda/envs/busco-5/config/
+    source activate busco-5
- # but we don't have writing permissions there
+    # in the busco-5 environment, AUGUSTUS_CONFIG_PATH is set to
- # not sure why we need writing permissions but it doesnt work anyway
+    # /scratch2/software/anaconda/envs/busco-5/config/
- # but we copied that dir to a place where we do have writing permissions:
+    # but we don't have writing permissions there
- # you may want to copy it to your own home
+    # not sure why we need writing permissions but it doesnt work anyway
- export AUGUSTUS_CONFIG_PATH="$HOME/busco/config/"
+    # but we copied that dir to a place where we do have writing permissions:
- INPUT='contigs_clean.fasta'
+    # you may want to copy it to your own home
- OUTDIR='busco5_contigs_clean_out'
+    export AUGUSTUS_CONFIG_PATH="$HOME/busco/config/"
- MODE='genome'
+    INPUT='contigs_clean.fasta'
- AUGUSTUS_SPECIES='leishmania_tarentolae'
+    OUTDIR='busco5_contigs_clean_out'
- # setting the lineage db
+    MODE='genome'
- ## the latest version (as of writing) is odb10
+    AUGUSTUS_SPECIES='leishmania_tarentolae'
- LINEAGEDB='/scratch5/db/Eukfinder/BUSCO/busco_downloads/lineages/eukaryota_odb10/'
+    # setting the lineage db
- ## busco v5 only works with odb10
+    ## the latest version (as of writing) is odb10
- ## it will not work with odb9
+    LINEAGEDB='/scratch5/db/Eukfinder/BUSCO/busco_downloads/lineages/eukaryota_odb10/'
- busco \
+    ## busco v5 only works with odb10
-     --in $INPUT \
+    ## it will not work with odb9
-     --out $OUTDIR \
+    busco \
-     --mode $MODE \
+        --in $INPUT \
-     --lineage_dataset $LINEAGEDB \
+        --out $OUTDIR \
-     --cpu 8 \
+        --mode $MODE \
-     --augustus \
+        --lineage_dataset $LINEAGEDB \
-     --augustus_species $AUGUSTUS_SPECIES \
+        --cpu 8 \
- conda deactivate
+        --augustus \
-Note: Take out the mitochondrial genome before running this analysis.
+        --augustus_species $AUGUSTUS_SPECIES \
+    conda deactivate
 **Note**: Take out the mitochondrial genome before running this analysis.