Squashed commit of the following:

commit 9542bcaa9036f585f56048cb12c4eee8d12319c0 Author: Benjamin Buchfink <[email protected]> Date: Sat Mar 18 11:17:52 2023 +0100 Fixed PAF bug. commit e6563b3dd023bd7bd4c81c7bce8ba7b655a635f0 Author: Benjamin Buchfink <[email protected]> Date: Sat Mar 18 10:47:09 2023 +0100 Fixed unaligned bug. commit 285afd5f33b8a58eb2d1d2cf3afff08063446f94 Author: Benjamin Buchfink <[email protected]> Date: Sat Mar 18 10:16:15 2023 +0100 Fixed macOS compiler error. commit 7dd350e04eb5626090313fe1af6d79e73711c6cc Author: Benjamin Buchfink <[email protected]> Date: Thu Mar 16 09:35:22 2023 +0100 Added switch to disable tls. commit 39c80484883ccbc31c439da1f37f5ef6dedb42f3 Merge: a11f8eda 21a32fc Author: Benjamin Buchfink <[email protected]> Date: Wed Mar 15 11:50:28 2023 +0100 Merge branch 'master' into dev commit a11f8eda395a1d7055d243346c1d786572c9343e Author: Benjamin Buchfink <[email protected]> Date: Wed Mar 15 11:49:23 2023 +0100 Disable sse for building blast. commit 857e96f539089474a66b37e35033ffcabd3bb8b3 Author: Benjamin Buchfink <[email protected]> Date: Tue Mar 14 12:54:52 2023 +0100 Fixed error. commit f8b3c28075c6a7a0bf2764389696de372dd8aa59 Author: Benjamin Buchfink <[email protected]> Date: Tue Mar 14 12:52:36 2023 +0100 Removed iostream includes. commit 24c930eed464fe08be2ab61f93042ce1a0fc804c Author: Benjamin Buchfink <[email protected]> Date: Tue Mar 14 11:29:03 2023 +0100 Added new dispatch code. commit b18d9e16043fc57122c095c91b29c0dcbf5f4b69 Author: Benjamin Buchfink <[email protected]> Date: Tue Mar 14 10:57:10 2023 +0100 Added new dispatch code. commit f1b05d05d0948f99f30c3e854b522546940d115e Author: Benjamin Buchfink <[email protected]> Date: Mon Mar 13 17:22:15 2023 +0100 Added new dispatch code. commit 8c66829f0df52eabaffe58215c730dae2af8b521 Author: Benjamin Buchfink <[email protected]> Date: Mon Mar 13 12:25:46 2023 +0100 Added new dispatch code. commit edb9ede545536c05ec47c16734a67a7c68b38033 Merge: 6b1658e2 c71b49c6 Author: Benjamin Buchfink <[email protected]> Date: Mon Mar 13 09:55:35 2023 +0100 Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev commit c71b49c6d16f6134b7068aa896be7961de02bce3 Author: Benjamin Buchfink <[email protected]> Date: Fri Mar 10 15:23:18 2023 +0100 Handle non-x86 case.
bbuchfink · Mar 18, 2023 · 0540f86 · 0540f86
1 parent 21a32fc
commit 0540f86
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -21,6 +21,7 @@ option(WITH_AVX512 "WITH_AVX512" OFF)
 option(WITH_DNA "WITH_DNA" OFF)
 option(WITH_MCL "WITH_MCL" OFF)
 option(WITH_MIMALLOC "WITH_MIMALLOC" OFF)
+option(USE_TLS "USE_TLS" OFF)
 set(MAX_SHAPE_LEN 19)
 set(BLAST_INCLUDE_DIR "" CACHE STRING "BLAST_INCLUDE_DIR")
 set(BLAST_LIBRARY_DIR "" CACHE STRING "BLAST_LIBRARY_DIR")
@@ -45,6 +46,10 @@ if(STRICT_BAND)
   add_definitions(-DSTRICT_BAND)
 endif()
 
+if(USE_TLS)
+  add_definitions(-DUSE_TLS)
+endif()
+
 if(SINGLE_THREADED)
   add_definitions(-DSINGLE_THREADED)
 endif()
@@ -148,7 +153,7 @@ endif()
 
 set(DISPATCH_OBJECTS
         "src/dp/swipe/banded_3frame_swipe.cpp"
-        "src/search/stage2.cpp"
+        "src/search/stage1_2.cpp"
         "src/tools/benchmark.cpp"
         "src/dp/swipe/swipe_wrapper.cpp"
         "src/masking/tantan.cpp"
@@ -175,6 +180,8 @@ if(X86)
     add_library(arch_avx512 OBJECT ${DISPATCH_OBJECTS})
     target_include_directories(arch_avx512 PRIVATE "${CMAKE_SOURCE_DIR}/src/lib")
   endif()
+  add_definitions(-DWITH_AVX2)
+  add_definitions(-DWITH_SSE4_1)
   if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
     target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__ -DEigen=Eigen_SSE4_1)
     target_compile_options(arch_avx2 PUBLIC -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 /arch:AVX2 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__ -DEigen=Eigen_AVX2)

diff --git a/Dockerfile b/Dockerfile
@@ -9,7 +9,7 @@ ADD . .
 
 RUN git clone https://github.com/ncbi/ncbi-cxx-toolkit-public.git
 WORKDIR ncbi-cxx-toolkit-public
-RUN ./cmake-configure --without-debug --with-projects="objtools/blast/seqdb_reader;objtools/blast/blastdb_format" --with-build-root=build
+RUN ./cmake-configure --without-debug --with-projects="objtools/blast/seqdb_reader;objtools/blast/blastdb_format" --with-build-root=build --with-features="-SSE"
 WORKDIR build/build
 RUN make -j4
 RUN cp /opt/diamond/ncbi-cxx-toolkit-public/build/inc/ncbiconf_unix.h /opt/diamond/ncbi-cxx-toolkit-public/include

diff --git a/src/ChangeLog b/src/ChangeLog
@@ -1,3 +1,11 @@
+[2.1.6]
+- Fixed compatibility issues on older systems without support for AVX2.
+- Fixed linker errors when compiled with `-DX86=OFF`.
+- Fixed a compiler error on macOS systems.
+- Fixed a bug that could cause missing tags in the XML output format and
+  unaligned queries not to be reported correctly.
+- Fixed a bug that caused the PAF output format not to work correctly.
+
 [2.1.5]
 - Disabled the use of frequency based seed masking when using the linear-time
   search feature with respect to the targets.

diff --git a/src/align/align.cpp b/src/align/align.cpp
@@ -198,7 +198,7 @@ TextBuffer* legacy_pipeline(const HitIterator::Hits& hits, Search::Config& cfg,
 
 	QueryMapper *mapper = new ExtensionPipeline::BandedSwipe::Pipeline(hits.query, hits.begin, hits.end, dp_stat, cfg);
 
-	task_timer timer("Initializing mapper", UINT_MAX);
+	TaskTimer timer("Initializing mapper", UINT_MAX);
 	mapper->init();
 	timer.finish();
 	mapper->run(stat, cfg);
@@ -293,7 +293,7 @@ void align_queries(Consumer* output_file, Search::Config& cfg)
 	const int64_t mem_limit = Util::String::interpret_number(config.memory_limit.get("16G"));
 
 	pair<BlockId, BlockId> query_range;
-	task_timer timer(nullptr, 3);
+	TaskTimer timer(nullptr, 3);
 
 	if (!cfg.blocked_processing && !cfg.iterated())
 		cfg.db->init_random_access(cfg.current_query_block, 0, false);

diff --git a/src/align/extend.cpp b/src/align/extend.cpp
@@ -252,7 +252,7 @@ pair<vector<Match>, Stats> extend(
 }
 
 pair<vector<Match>, Stats> extend(BlockId query_id, Search::Hit* begin, Search::Hit* end, const Search::Config &cfg, Statistics &stat, DP::Flags flags) {
-	task_timer timer(flag_any(flags, DP::Flags::PARALLEL) ? config.target_parallel_verbosity : UINT_MAX);
+	TaskTimer timer(flag_any(flags, DP::Flags::PARALLEL) ? config.target_parallel_verbosity : UINT_MAX);
 	timer.go("Loading seed hits");
 	SeedHitList l = load_hits(begin, end, cfg.target->seqs());
 	stat.inc(Statistics::TARGET_HITS0, l.target_block_ids.size());

diff --git a/src/align/extend_chunk.h b/src/align/extend_chunk.h
@@ -29,7 +29,7 @@ pair<vector<Target>, Stats> extend(BlockId query_id,
 	static const Loc GAPPED_FILTER_MIN_QLEN = 85;
 	const int64_t n = seed_hits_end - seed_hits;
 	stat.inc(Statistics::TARGET_HITS2, n);
-	task_timer timer(flag_any(flags, DP::Flags::PARALLEL) ? config.target_parallel_verbosity : UINT_MAX);
+	TaskTimer timer(flag_any(flags, DP::Flags::PARALLEL) ? config.target_parallel_verbosity : UINT_MAX);
 
 	if (cfg.lazy_masking && !config.global_ranking_targets)
 		stat.inc(Statistics::MASKED_LAZY, lazy_masking(target_block_ids, target_block_ids + n, *cfg.target, cfg.target_masking));

diff --git a/src/align/gapped_filter.cpp b/src/align/gapped_filter.cpp
@@ -34,7 +34,7 @@ using std::pair;
 
 namespace Extension {
 
-int gapped_filter(const SeedHit &hit, const LongScoreProfile<int8_t> *query_profile, const Sequence &target, int band, int window, std::function<decltype(DP::ARCH_GENERIC::scan_diags128)> f) {	
+int gapped_filter(const SeedHit &hit, const LongScoreProfile<int8_t> *query_profile, const Sequence &target, int band, int window, std::function<decltype(DP::scan_diags128)> f) {	
 	const int slen = (int)target.length();
 	const int d = std::max(hit.diag() - band / 2, -(slen - 1)),
 		j0 = std::max(hit.j - window, 0),

diff --git a/src/align/gapped_score.cpp b/src/align/gapped_score.cpp
@@ -212,7 +212,7 @@ pair<vector<Target>, Stats> align(const vector<WorkTarget> &targets, const Seque
 			LongScoreProfile<int16_t> p;
 			LongScoreProfile<int8_t> p8;
 			const bool hauser_cbs = ::Stats::CBS::hauser(config.comp_based_stats);
-			task_timer timer;
+			TaskTimer timer;
 			p = DP::make_profile16(query_seq[frame], hauser_cbs ? query_cb[frame].int8.data() : nullptr, 0);
 			p8 = DP::make_profile8(query_seq[frame], hauser_cbs ? query_cb[frame].int8.data() : nullptr, 0);
 			LongScoreProfile<int16_t> p_rev(p.reverse());

diff --git a/src/align/global_ranking/extend.cpp b/src/align/global_ranking/extend.cpp
@@ -89,7 +89,7 @@ void align_worker(InputFile* query_list, const TargetMap* db2block_id, const Sea
 }
 
 void extend(SequenceFile& db, TempFile& merged_query_list, BitVector& ranking_db_filter, Search::Config& cfg, Consumer& master_out) {
-	task_timer timer("Loading reference sequences");
+	TaskTimer timer("Loading reference sequences");
 	InputFile query_list(merged_query_list);
 	db.set_seqinfo_ptr(0);
 	cfg.target.reset(db.load_seqs(INT64_MAX, &ranking_db_filter, SequenceFile::LoadFlags::SEQS));
@@ -178,7 +178,7 @@ static BitVector db_filter(const Search::Config::RankingTable& table, size_t db_
 }
 
 void extend(Search::Config& cfg, Consumer& out) {
-	task_timer timer("Listing target sequences");
+	TaskTimer timer("Listing target sequences");
 	const BitVector filter = db_filter(*cfg.ranking_table, cfg.db->sequence_count());
 	timer.go("Loading target sequences");
 	cfg.db->set_seqinfo_ptr(0);

diff --git a/src/align/global_ranking/table.cpp b/src/align/global_ranking/table.cpp
@@ -152,7 +152,7 @@ void update_table(Search::Config& cfg) {
 	log_stream << "Seed hits = " << hits.size() << endl;
 	if (hits.size() == 0)
 		return;
-	task_timer timer("Sorting seed hits");
+	TaskTimer timer("Sorting seed hits");
 #if _MSC_FULL_VER == 191627042
 	merge_sort(hits.begin(), hits.end(), config.threads_, Search::Hit::CmpQueryTarget());
 #else

diff --git a/src/align/legacy/banded_swipe_pipeline.cpp b/src/align/legacy/banded_swipe_pipeline.cpp
@@ -181,7 +181,7 @@ void build_ranking_worker(PtrVector<::Target>::iterator begin, PtrVector<::Targe
 
 void Pipeline::run(Statistics &stat, const Search::Config& cfg)
 {
-	task_timer timer("Init banded swipe pipeline", target_parallel ? 3 : UINT_MAX);
+	TaskTimer timer("Init banded swipe pipeline", target_parallel ? 3 : UINT_MAX);
 	Config::set_option(config.padding, 32);
 	if (n_targets() == 0)
 		return;

diff --git a/src/align/legacy/query_mapper.cpp b/src/align/legacy/query_mapper.cpp
@@ -99,7 +99,7 @@ QueryMapper::QueryMapper(size_t query_id, Search::Hit* begin, Search::Hit* end,
 void QueryMapper::init()
 {
 	if(config.log_query)
-		std::cout << "Query = " << metadata.query->ids()[query_id] << '\t' << query_id << std::endl;
+		message_stream << "Query = " << metadata.query->ids()[query_id] << '\t' << query_id << std::endl;
 	if (Stats::CBS::hauser(config.comp_based_stats))
 		for (int i = 0; i < align_mode.query_contexts; ++i)
 			query_cb.emplace_back(query_seq(i));

diff --git a/src/align/output.cpp b/src/align/output.cpp
@@ -37,7 +37,7 @@ TextBuffer* generate_output(vector<Match> &targets, const Extension::Stats& stat
 	std::unique_ptr<OutputFormat> f(cfg.output_format->clone());
 	size_t seek_pos = 0;
 	unsigned n_hsp = 0, hit_hsps = 0;
-	Output::Info info{ cfg.query->seq_info(query_block_id), !targets.empty(), cfg.db.get(), *out, stats };
+	Output::Info info{ cfg.query->seq_info(query_block_id), targets.empty(), cfg.db.get(), *out, stats };
 	TranslatedSequence query = query_seqs.translated_seq(align_mode.query_translated ? cfg.query->source_seqs()[query_block_id] : query_seqs[query_block_id], query_block_id * align_mode.query_contexts);
 	const char *query_title = cfg.query->ids()[query_block_id];
 	const double query_self_aln_score = cfg.query->has_self_aln() ? cfg.query->self_aln_score(query_block_id) : 0.0;

diff --git a/src/align/ungapped.cpp b/src/align/ungapped.cpp
@@ -62,7 +62,7 @@ WorkTarget::WorkTarget(BlockId block_id, const Sequence& seq, int query_len, con
 
 WorkTarget ungapped_stage(FlatArray<SeedHit>::DataIterator begin, FlatArray<SeedHit>::DataIterator end, const Sequence *query_seq, const Bias_correction *query_cb, const ::Stats::Composition& query_comp, const int16_t** query_matrix, uint32_t block_id, Statistics& stat, const Block& targets, const Mode mode) {
 	array<vector<DiagonalSegment>, MAX_CONTEXT> diagonal_segments;
-	task_timer timer;
+	TaskTimer timer;
 	const SequenceSet& ref_seqs = targets.seqs(), &ref_seqs_unmasked = targets.unmasked_seqs();
 	const bool masking = config.comp_based_stats == ::Stats::CBS::COMP_BASED_STATS_AND_MATRIX_ADJUST ? ::Stats::use_seg_masking(query_seq[0], ref_seqs_unmasked[block_id]) : true;
 	WorkTarget target(block_id, masking ? ref_seqs[block_id] : ref_seqs_unmasked[block_id], ::Stats::count_true_aa(query_seq[0]), query_comp, query_matrix);

diff --git a/src/basic/basic.cpp b/src/basic/basic.cpp
@@ -29,7 +29,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "../util/util.h"
 #include "../stats/standard_matrix.h"
 
-const char* Const::version_string = "2.1.5";
+const char* Const::version_string = "2.1.6";
 using std::string;
 using std::vector;
 using std::count;

diff --git a/src/basic/config.cpp b/src/basic/config.cpp
@@ -21,6 +21,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ****/
 
 #include <memory>
+#include <iostream>
 #include <cstdlib>
 #include <sys/stat.h>
 #include <exception>
@@ -50,12 +51,12 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 using std::thread;
 using std::stringstream;
 using std::endl;
-using std::cerr;
 using std::ostream;
-using std::cout;
 using std::unique_ptr;
 using std::string;
 using std::pair;
+using std::cout;
+using std::cerr;
 
 const EMap<Sensitivity> EnumTraits<Sensitivity>::to_string = {
 	{ Sensitivity::FASTER, "faster" },
@@ -115,61 +116,14 @@ pair<double, int> block_size(int64_t memory_limit, Sensitivity s, bool lin) {
 	return { std::max(b, 0.001), c };
 }
 
-void print_warnings() {
-	if (config.sensitivity >= Sensitivity::VERY_SENSITIVE || config.verbosity == 0 || config.swipe_all)
-		return;
-	if (config.command != Config::blastp && config.command != Config::blastx && config.command != Config::blastn)
-		return;
-	const double ram = total_ram();
-	unsigned b = 2, c = 4;
-	stringstream msg;
-	if (config.sensitivity >= Sensitivity::SENSITIVE) {
-		if (ram >= 63) {
-			c = 1;
-			if(c < config.lowmem_)
-				msg << "use this parameter for better performance: -c1";
-		}
-	}
-	else {
-		if (ram >= 511) {
-			b = 12;
-			c = 1;
-		}
-		else if (ram >= 255) {
-			b = 8;
-			c = 1;
-		}
-		else if (ram >= 127) {
-			b = 5;
-			c = 1;
-		}
-		else if (ram >= 63) {
-			b = 6;
-		}
-		else if (ram >= 31) {
-			b = 4;
-		}
-		if ((b > 2 && b > config.chunk_size) || c < config.lowmem_) {
-			msg << "increase the block size for better performance using these parameters : -b" << b;
-			if (c != 4)
-				msg << " -c" << c;
-		}
-	}
-	if (!msg.str().empty()) {
-		set_color(Color::YELLOW, true);
-		cerr << "The host system is detected to have " << (size_t)ram << " GB of RAM. It is recommended to " << msg.str() << endl;
-		reset_color(true);
-	}
-}
-
-template<typename _t>
-_t set_string_option(const string& s, const string& name, const vector<pair<string, _t>>& values) {
+template<typename T>
+T set_string_option(const string& s, const string& name, const vector<pair<string, T>>& values) {
 	if (s.empty())
-		return (_t)0;
+		return (T)0;
 	for (auto& i : values)
 		if (s == i.first)
 			return i.second;
-	throw std::runtime_error("Invalid argument for option " + name + ". Allowed values are:" + std::accumulate(values.begin(), values.end(), string(), [](const string& s, const pair<string, _t>& v) { return s + ' ' + v.first; }));
+	throw std::runtime_error("Invalid argument for option " + name + ". Allowed values are:" + std::accumulate(values.begin(), values.end(), string(), [](const string& s, const pair<string, T>& v) { return s + ' ' + v.first; }));
 }
 
 void Config::set_sens(Sensitivity sens) {

diff --git a/src/basic/const.h b/src/basic/const.h
@@ -25,7 +25,7 @@ struct Const
 {
 
 	enum {
-		build_version = 159,
+		build_version = 160,
 #ifdef SINGLE_THREADED
 		seedp_bits = 0,
 #else

diff --git a/src/chaining/greedy_align.cpp b/src/chaining/greedy_align.cpp
@@ -24,6 +24,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <map>
 #include <list>
 #include <set>
+#include <iostream>
 #include "../basic/sequence.h"
 #include "../basic/match.h"
 #include "../stats/score_matrix.h"

diff --git a/src/cluster/cascaded/cascaded.cpp b/src/cluster/cascaded/cascaded.cpp
@@ -77,7 +77,7 @@ vector<SuperBlockId> cluster(shared_ptr<SequenceFile>& db, const shared_ptr<BitV
 	Search::run(db, nullptr, callback, filter);
 
 	message_stream << "Finished search. #Edges: " << callback->count << endl;
-	task_timer timer("Allocating buffers");
+	TaskTimer timer("Allocating buffers");
 	vector<Edge> edges(callback->count);
 	timer.go("Loading edges");
 	InputFile f(callback->edge_file);
@@ -113,7 +113,7 @@ vector<SuperBlockId> cascaded(shared_ptr<SequenceFile>& db, bool linear) {
 	iota(centroids.begin(), centroids.end(), 0);
 
 	for (int i = 0; i < (int)steps.size(); i++) {
-		task_timer timer;
+		TaskTimer timer;
 		config.lin_stage1 = ends_with(steps[i], "_lin");
 		config.sensitivity = from_string<Sensitivity>(rstrip(steps[i], "_lin"));
 		tie(centroids, *oid_filter) = update_clustering(*oid_filter,

diff --git a/src/cluster/cascaded/recluster.cpp b/src/cluster/cascaded/recluster.cpp
@@ -41,7 +41,7 @@ using std::pair;
 namespace Cluster {
 
 static vector<OId> recluster(shared_ptr<SequenceFile>& db, const vector<OId>& clustering, int iteration) {
-	task_timer timer(("*** Initializing recluster iteration " + to_string(iteration + 1)).c_str());
+	TaskTimer timer(("*** Initializing recluster iteration " + to_string(iteration + 1)).c_str());
 
 	FlatArray<OId> clusters;
 	vector<OId> centroids;
@@ -178,7 +178,7 @@ void recluster() {
 	//config.strict_gvc = true;
 	message_stream << "Coverage cutoff: " << config.member_cover << '%' << endl;
 
-	task_timer timer("Opening the database");
+	TaskTimer timer("Opening the database");
 	shared_ptr<SequenceFile> db(SequenceFile::auto_create({ config.database }, SequenceFile::Flags::NEED_LETTER_COUNT | SequenceFile::Flags::ACC_TO_OID_MAPPING | SequenceFile::Flags::OID_TO_ACC_MAPPING, SequenceFile::Metadata()));
 	config.db_size = db->letters();
 	timer.finish();

diff --git a/src/cluster/cascaded/wrapper.cpp b/src/cluster/cascaded/wrapper.cpp
@@ -34,7 +34,6 @@ using std::string;
 using std::vector;
 using std::ostream;
 using std::ofstream;
-using std::cout;
 using std::numeric_limits;
 using std::tuple;
 using std::get;
@@ -67,7 +66,7 @@ struct Config {
 	double                              block_size;
 	std::unique_ptr<OutputFormat>       output_format;
 	std::shared_ptr<FastaFile>          centroids;
-	task_timer                          total_time;
+	TaskTimer                          total_time;
 	int64_t                             seqs_processed;
 	int64_t                             letters_processed;
 	std::vector<OId>                    centroid2oid;
@@ -158,8 +157,8 @@ void Cascaded::run() {
 	config.database.require();
 	init_thresholds();
 	config.hamming_ext = config.approx_min_id >= 50.0;
-	task_timer total_time;
-	task_timer timer("Opening the input file");
+	TaskTimer total_time;
+	TaskTimer timer("Opening the input file");
 	shared_ptr<SequenceFile> db(SequenceFile::auto_create({ config.database }, SequenceFile::Flags::NEED_LETTER_COUNT | SequenceFile::Flags::OID_TO_ACC_MAPPING));
 	if (db->type() == SequenceFile::Type::BLAST)
 		throw std::runtime_error("Clustering is not supported for BLAST databases.");

diff --git a/src/cluster/helpers.cpp b/src/cluster/helpers.cpp
@@ -33,7 +33,6 @@ using std::pair;
 using std::endl;
 using std::vector;
 using std::ofstream;
-using std::cout;
 using std::ostream;
 using std::runtime_error;
 using std::string;

diff --git a/src/cluster/incremental/common.h b/src/cluster/incremental/common.h
@@ -17,7 +17,7 @@ struct Config {
 	std::unique_ptr<SequenceFile>       db;
 	std::shared_ptr<FastaFile>          centroids;
 	std::unique_ptr<Util::Tsv::File>    output_file;
-	task_timer                          total_time;
+	TaskTimer                          total_time;
 	int64_t                             seqs_processed;
 	int64_t                             letters_processed;
 	std::vector<CentroidId>             oid2centroid;

diff --git a/src/cluster/incremental/run.cpp b/src/cluster/incremental/run.cpp
@@ -43,7 +43,7 @@ struct BestCentroid : public Consumer, public vector<OId> {
 
 static void self_align(Block& block, Config& cfg) {
 	using Edge = Util::Algo::Edge<SuperBlockId>;
-	task_timer timer(("CLUSTER Searching " + std::to_string(block.seqs().size()) + " unaligned sequences").c_str(), cfg.message_stream);
+	TaskTimer timer(("CLUSTER Searching " + std::to_string(block.seqs().size()) + " unaligned sequences").c_str(), cfg.message_stream);
 	shared_ptr<Callback> neighbors(new Callback());
 	shared_ptr<BlockWrapper> unaligned_wrapper(new BlockWrapper(block));
 	config.self = true;
@@ -101,7 +101,7 @@ static void search_vs_centroids(Block& block, const int round, Config& cfg) {
 		cfg.message_stream << "CLUSTER searching vs. centroids sensitivity = " << to_string(cfg.sens[round])
 		<< " #sequences = " << block.seqs().size() << " , #centroids = " << cfg.centroids->sequence_count() << endl;
 	cfg.status_msg();
-	task_timer timer(("Searching " + std::to_string(block.seqs().size()) + " against centroid sequences (" + to_string(cfg.sens[round]) + ")").c_str(), cfg.message_stream);
+	TaskTimer timer(("Searching " + std::to_string(block.seqs().size()) + " against centroid sequences (" + to_string(cfg.sens[round]) + ")").c_str(), cfg.message_stream);
 	shared_ptr<BlockWrapper> block_wrapper(new BlockWrapper(block));
 	shared_ptr<BestCentroid> best_centroid(new BestCentroid(block.seqs().size()));
 	config.self = false;
@@ -147,7 +147,7 @@ void Algo::run() {
 	if (!config.resume.empty())
 		cfg.load_state();
 
-	task_timer timer("CLUSTER Opening the input file", cfg.message_stream);
+	TaskTimer timer("CLUSTER Opening the input file", cfg.message_stream);
 	const int64_t block_size = (int64_t)(cfg.block_size * 1e9), cache_limit = 0; // block_size;
 	config.output_format = { "edge" };
 	unique_ptr<Block> block;