From ea47a9229d9c37c223209767085d1bdde19099d6 Mon Sep 17 00:00:00 2001 From: Martin Steinegger Date: Sat, 11 Jan 2025 03:50:05 +0900 Subject: [PATCH] Squashed 'lib/mmseqs/' changes from 416fc728..934db4f9 934db4f9 Adjust createindex to handle maskNlower 0266ea53 Add better error message c5ca4c3f Improve error message 6c267ec1 Improve error message git-subtree-dir: lib/mmseqs git-subtree-split: 934db4f98e8d75427d83f47a606b5d7528f92606 --- src/prefiltering/PrefilteringIndexReader.cpp | 4 ++-- src/prefiltering/ungappedprefilter.cpp | 3 ++- src/util/gpuserver.cpp | 3 ++- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/prefiltering/PrefilteringIndexReader.cpp b/src/prefiltering/PrefilteringIndexReader.cpp index e654ff6e..65215f4e 100644 --- a/src/prefiltering/PrefilteringIndexReader.cpp +++ b/src/prefiltering/PrefilteringIndexReader.cpp @@ -228,8 +228,8 @@ void PrefilteringIndexReader::createIndexFile(const std::string &outDB, IndexTable indexTable(adjustAlphabetSize, kmerSize, false); SequenceLookup *sequenceLookup = NULL; IndexBuilder::fillDatabase(&indexTable, - (maskMode == 1 || maskLowerCase == 1) ? &sequenceLookup : NULL, - (maskMode == 0 && maskLowerCase == 0) ? &sequenceLookup : NULL, + (maskMode == 1 || maskNrepeats > 0 || maskLowerCase == 1) ? &sequenceLookup : NULL, + (maskMode == 0 && maskNrepeats == 0 && maskLowerCase == 0) ? &sequenceLookup : NULL, *subMat, s3, s2, &seq, dbr1, dbFrom, dbFrom + dbSize, kmerThr, maskMode, maskLowerCase, maskProb, maskNrepeats, targetSearchMode); indexTable.printStatistics(subMat->num2aa); diff --git a/src/prefiltering/ungappedprefilter.cpp b/src/prefiltering/ungappedprefilter.cpp index d84b63a7..f07fed84 100644 --- a/src/prefiltering/ungappedprefilter.cpp +++ b/src/prefiltering/ungappedprefilter.cpp @@ -404,7 +404,8 @@ int prefilterInternal(int argc, const char **argv, const Command &command, int m if (par.gpu == true) { const bool isGpuDb = DBReader::getExtendedDbtype(tdbr->getDbtype()) & Parameters::DBTYPE_EXTENDED_GPU; if (isGpuDb == false) { - Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db2) << " is not a valid GPU database\n"; + Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db2) << " is not a valid GPU database\n" + << "Please call: makepaddedseqdb " << FileUtil::baseName(par.db2) << " " << FileUtil::baseName(par.db2) << "_pad\n"; EXIT(EXIT_FAILURE); } } diff --git a/src/util/gpuserver.cpp b/src/util/gpuserver.cpp index 657edeba..db4887f2 100644 --- a/src/util/gpuserver.cpp +++ b/src/util/gpuserver.cpp @@ -31,7 +31,8 @@ int gpuserver(int argc, const char **argv, const Command& command) { const bool isGpuDb = DBReader::getExtendedDbtype(dbr->getDbtype()) & Parameters::DBTYPE_EXTENDED_GPU; if (isGpuDb == false) { - Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db1) << " is not a valid GPU database\n"; + Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db1) << " is not a valid GPU database\n" + << "Please call: makepaddedseqdb " << FileUtil::baseName(par.db2) << " " << FileUtil::baseName(par.db2) << "_pad\n"; EXIT(EXIT_FAILURE); }