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Skip hash table size estimation if already done #450

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Skip hash table size estimation if already done #450

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961adf5
Skip hash table size estimation if already done
kim-fehl May 16, 2021
f64437d
Skip hash table size estimation if already done
kim-fehl May 16, 2021
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51 changes: 29 additions & 22 deletions scripts/build_kraken2_db.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -64,14 +64,14 @@ then
KRAKEN2XFLAG="-X"
fi

echo "Creating sequence ID to taxonomy ID map (step 1)..."
if [ -d "library/added" ]; then
find library/added/ -name 'prelim_map_*.txt' | xargs cat > library/added/prelim_map.txt
fi
seqid2taxid_map_file=seqid2taxid.map
if [ -e "$seqid2taxid_map_file" ]; then
echo "Sequence ID to taxonomy ID map already present, skipping map creation."
echo "Sequence ID to taxonomy ID map already present, skipping map creation (step 1)."
else
echo "Creating sequence ID to taxonomy ID map (step 1)..."
if [ -d "library/added" ]; then
find library/added/ -name 'prelim_map_*.txt' | xargs cat > library/added/prelim_map.txt
fi
step_time=$(get_current_time)
find library/ -maxdepth 2 -name prelim_map.txt | xargs cat > taxonomy/prelim_map.txt
if [ ! -s "taxonomy/prelim_map.txt" ]; then
Expand All @@ -95,28 +95,35 @@ else
echo "Sequence ID to taxonomy ID map complete. [$(report_time_elapsed $step_time)]"
fi

echo "Estimating required capacity (step 2)..."

step_time=$(get_current_time)
estimate=$(list_sequence_files | xargs -0 cat | estimate_capacity -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE -p $KRAKEN2_THREAD_CT $KRAKEN2XFLAG )
# Slight upward adjustment of distinct minimizer estimate to protect
# against crash w/ small reference sets
estimate=$(( estimate + 8192 ))
required_capacity=$(perl -le 'print int(shift() / shift())' $estimate $KRAKEN2_LOAD_FACTOR);

echo "Estimated hash table requirement: $(( required_capacity * 4 )) bytes"

required_capacity_file="required_capacity.txt"
max_db_flag=""
if [ -n "$KRAKEN2_MAX_DB_SIZE" ]
then
if (( KRAKEN2_MAX_DB_SIZE < (required_capacity * 4) ))
if [ -e "$required_capacity_file" ]; then
echo "Required capacity has already been estimated, skipping estimation (step 2)."
required_capacity=$( < $required_capacity_file )
else
echo "Estimating required capacity (step 2)..."

step_time=$(get_current_time)
estimate=$(list_sequence_files | xargs -0 cat | estimate_capacity -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE -p $KRAKEN2_THREAD_CT $KRAKEN2XFLAG )
# Slight upward adjustment of distinct minimizer estimate to protect
# against crash w/ small reference sets
estimate=$(( estimate + 8192 ))
required_capacity=$(perl -le 'print int(shift() / shift())' $estimate $KRAKEN2_LOAD_FACTOR);
echo $required_capacity > $required_capacity_file

if [ -n "$KRAKEN2_MAX_DB_SIZE" ]
then
max_db_flag="-M $(perl -le 'print int(shift() / 4)' $KRAKEN2_MAX_DB_SIZE)"
echo "Specifying lower maximum hash table size of $KRAKEN2_MAX_DB_SIZE bytes"
if (( KRAKEN2_MAX_DB_SIZE < (required_capacity * 4) ))
then
max_db_flag="-M $(perl -le 'print int(shift() / 4)' $KRAKEN2_MAX_DB_SIZE)"
echo "Specifying lower maximum hash table size of $KRAKEN2_MAX_DB_SIZE bytes"
fi
fi

echo "Capacity estimation complete. [$(report_time_elapsed $step_time)]"
fi
echo "Estimated hash table requirement: $(( required_capacity * 4 )) bytes"

echo "Capacity estimation complete. [$(report_time_elapsed $step_time)]"

echo "Building database files (step 3)..."

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