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adding the phrog command #39

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Merged
linsalrob merged 1 commit into from
Aug 6, 2026
Merged

adding the phrog command #39

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16 changes: 14 additions & 2 deletions pawsey_shortread/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ nano DEFINITIONS.sh
```


# 2. Check the names of your files.
## 2. Check the names of your files.

We need to be consistent with the names of our files, so we start by looking at the file names.

Expand Down Expand Up @@ -213,7 +213,19 @@ grep 'primary mapped' slurm_output/sixteen_s/*out | perl -ne 'm/(\d+\.\d+)\%/; p
grep 'primary mapped' slurm_output/sixteen_s/*out | perl -ne 'm/(\d+\.\d+)\%/; print "$1\n"' | awk '{s+=$1} END {print s/NR}'
```

## 15. VAMB
## 15. PHROGs

We can use the mmseqs analysis to find PHROGs. We have a mapping between the UniProt IDs and the PHOG IDs which we use to map
similarities.
Comment on lines +218 to +219

First, we create a new mmseqs-derived output file with the PHROG IDs, and then we count the PHROG IDs in each sample. The output is in the `phrogs` directory.

```
PHROGJOB=$(sbatch --parsable --dependency=afterok:$MMSEQSJOB --array=1-$NUM_R1_READS:1 $PAWSEY_SRC/mmseqs_add_phrog_function.slurm)
sbatch --parsable --dependency=afterok:$PHROGJOB $PAWSEY_SRC/count_phrog_functions.slurm
Comment on lines +224 to +225
```

## 16. VAMB

Please note: this section of the README needs some improvement, because I have not used the different pieces in a while.

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