From 57cc1cf829aa6d9977c5988c74c576fa7ccd4521 Mon Sep 17 00:00:00 2001 From: Annika Jochheim Date: Tue, 16 Apr 2024 22:11:28 +0200 Subject: [PATCH] proteinaln2nucl did not use the threads parameter --- data/guidedNuclAssemble.sh | 2 +- src/workflow/GuidedNuclassembler.cpp | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/data/guidedNuclAssemble.sh b/data/guidedNuclAssemble.sh index 4b00f73c..d7e2448b 100644 --- a/data/guidedNuclAssemble.sh +++ b/data/guidedNuclAssemble.sh @@ -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" diff --git a/src/workflow/GuidedNuclassembler.cpp b/src/workflow/GuidedNuclassembler.cpp index 58061341..25689045 100644 --- a/src/workflow/GuidedNuclassembler.cpp +++ b/src/workflow/GuidedNuclassembler.cpp @@ -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;