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proteinaln2nucl did not use the threads parameter
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AnnSeidel committed Apr 16, 2024
1 parent ff8fc36 commit 57cc1cf
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Showing 2 changed files with 3 additions and 1 deletion.
2 changes: 1 addition & 1 deletion data/guidedNuclAssemble.sh
Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ while [ $STEP -lt $NUM_IT ]; do

# 3. Ungapped alignment protein 2 nucl
if notExists "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_$STEP.done"; then
"$MMSEQS" proteinaln2nucl "$INPUT_NUCL" "$INPUT_NUCL" "$INPUT_AA" "$INPUT_AA" "${TMP_PATH_GUIDED_ASSEMBLY}/aln_$STEP" "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_$STEP" \
"$MMSEQS" proteinaln2nucl "$INPUT_NUCL" "$INPUT_NUCL" "$INPUT_AA" "$INPUT_AA" "${TMP_PATH_GUIDED_ASSEMBLY}/aln_$STEP" "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_$STEP" "${PROTEIN_ALN_2_NUCL_PAR}" \
|| fail "Ungapped alignment 2 nucl step died"
deleteIncremental "$PREV_ALN_NUCL"
touch "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_${STEP}.done"
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2 changes: 2 additions & 0 deletions src/workflow/GuidedNuclassembler.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -157,6 +157,8 @@ int guidedNuclAssemble(int argc, const char **argv, const Command &command) {
bool addBacktrace = par.addBacktrace;
par.addBacktrace = true;
cmd.addVariable("UNGAPPED_ALN_PAR", par.createParameterString(par.rescorediagonal).c_str());
cmd.addVariable("PROTEIN_ALN_2_NUCL_PAR", par.createParameterString(par.proteinaln2nucl).c_str());


// # 3. Assembly: Extend by left and right extension
par.seqIdThr = par.multiSeqIdThr.nucleotides;
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