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alexdobin / STAR

RNA-seq aligner
MIT License
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Installation issue #371

Closed kibriadurlav closed 6 years ago

kibriadurlav commented 6 years ago

Hi @alexdobin

I tried installing from source using git, but when I enter make STAR, I am having following error,

make star Makefile:91: Depend.list: No such file or directory make -C htslib lib-static make[1]: Entering directory '/home/kibria/STAR/source/htslib' cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "0.0.1"' > version.h cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o sam.o sam.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c cram/vlen.c: In function ‘vflen’: cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] int i; ^ cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a make[1]: Leaving directory '/home/kibria/STAR/source/htslib' echo Chain.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp BAMoutput.cpp ReadAlign_outputTranscriptSAM.cpp readLoad.cpp sjdbInsertJunctions.cpp Stats.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp Parameters_readSAMheader.cpp BAMbinSortByCoordinate.cpp Genome_insertSequences.cpp Transcriptome_quantAlign.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp Quantifications.cpp ReadAlignChunk.cpp Transcriptome.cpp PackedArray.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp ReadAlign_calcCIGAR.cpp genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp sjSplitAlign.cpp ReadAlign_chimericDetection.cpp BAMfunctions.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp binarySearch2.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp ReadAlign_outputTranscriptSJ.cpp SequenceFuns.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp ReadAlign_oneRead.cpp ReadAlign_CIGAR.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp extendAlign.cpp Transcript_alignScore.cpp sortSuffixesBucket.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp bam_cat.c Chain.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp BAMoutput.cpp ReadAlign_outputTranscriptSAM.cpp readLoad.cpp sjdbInsertJunctions.cpp Stats.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp Parameters_readSAMheader.cpp BAMbinSortByCoordinate.cpp Genome_insertSequences.cpp Transcriptome_quantAlign.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp Quantifications.cpp ReadAlignChunk.cpp Transcriptome.cpp PackedArray.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp ReadAlign_calcCIGAR.cpp genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp sjSplitAlign.cpp ReadAlign_chimericDetection.cpp BAMfunctions.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp binarySearch2.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp ReadAlign_outputTranscriptSJ.cpp SequenceFuns.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp ReadAlign_oneRead.cpp ReadAlign_CIGAR.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp extendAlign.cpp Transcript_alignScore.cpp sortSuffixesBucket.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp bam_cat.c 'rm' -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Feb 7 11:08:06 +06 2018 :/home/kibria/STAR/source"' -MM Chain.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp BAMoutput.cpp ReadAlign_outputTranscriptSAM.cpp readLoad.cpp sjdbInsertJunctions.cpp Stats.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp Parameters_readSAMheader.cpp BAMbinSortByCoordinate.cpp Genome_insertSequences.cpp Transcriptome_quantAlign.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp Quantifications.cpp ReadAlignChunk.cpp Transcriptome.cpp PackedArray.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp sjdbLoadFromStream.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp ReadAlign_calcCIGAR.cpp genomeGenerate.cpp outputSJ.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp sjSplitAlign.cpp ReadAlign_chimericDetection.cpp BAMfunctions.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp binarySearch2.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp ReadAlign_outputTranscriptSJ.cpp SequenceFuns.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp ReadAlign_oneRead.cpp ReadAlign_CIGAR.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp extendAlign.cpp Transcript_alignScore.cpp sortSuffixesBucket.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++: warning: htslib: linker input file unused because linking not done make: *** No rule to make target 'star'. Stop. root@OptiPlex-3020:/home/kibria/STAR/source#

Any help will be highly appreciated!

Cheers,

Kibria.

khllkcm commented 6 years ago

Instead of make star try make STAR. Build targets are case-sensitive.

kibriadurlav commented 6 years ago

Yeah I did with make STAR, but still that happens. If I remove line 20 from the bin Makefile, then also I receive an error.

khllkcm commented 6 years ago

Can you post the specific error message you got after running make STAR?

kibriadurlav commented 6 years ago

Hi @khllkcm,

So, today I added line 20, and put make STAR, and guess what, looks like it worked! Check following message,

make STAR g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Parameters.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' InOutStreams.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' SequenceFuns.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Genome.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Chain.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Stats.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Transcript.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Transcript_alignScore.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_storeAligns.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_stitchPieces.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_multMapSelect.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_mapOneRead.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' readLoad.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlignChunk.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlignChunk_processChunks.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlignChunk_mapChunk.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' OutSJ.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' outputSJ.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' blocksOverlap.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ThreadControl.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sysRemoveDir.cpp sysRemoveDir.cpp:7:58: warning: unused parameter ‘sb’ [-Wunused-parameter] int removeFileOrDir(const char fpath,const struct stat sb, int typeflag, struct FTW ftwbuf) { ^ sysRemoveDir.cpp:7:88: warning: unused parameter ‘ftwbuf’ [-Wunused-parameter] int removeFileOrDir(const char fpath,const struct stat sb, int typeflag, struct FTW ftwbuf) { ^ g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_maxMappableLength2strands.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' binarySearch2.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_outputAlignments.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_outputTranscriptSAM.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_outputTranscriptSJ.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_assignAlignToWindow.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_oneRead.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_stitchWindowSeeds.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_chimericDetection.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' stitchWindowAligns.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' extendAlign.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' stitchAlignToTranscript.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' alignSmithWaterman.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' genomeGenerate.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' genomeParametersWrite.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' genomeScanFastaFiles.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' genomeSAindex.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Genome_insertSequences.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' insertSeqSA.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' funCompareUintAndSuffixes.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sortSuffixesBucket.cpp sortSuffixesBucket.cpp: In function ‘void sortSuffixesBucket(char, void, int, int)’: sortSuffixesBucket.cpp:27:43: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] uint64_t iprev=(uint64_t)(ind+0indSkip); ^ sortSuffixesBucket.cpp:31:37: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] if ((uint64_t)(ind+idindSkip)==iprev) ^ sortSuffixesBucket.cpp:43:43: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] iprev=(uint64_t)(ind+idindSkip); ^ sortSuffixesBucket.cpp:62:49: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] charCount[G[(uint64_t)(ind+idindSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:62:57: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] charCount[G[(uint64_t)(ind+idindSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:62:72: warning: array subscript has type ‘char’ [-Wchar-subscripts] charCount[G[(uint64_t)(ind+idindSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:85:50: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] char c=G[(uint64_t)(ind+idindSkip+8) + charShift]; ^ sortSuffixesBucket.cpp:85:58: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] char c=G[(uint64_t)(ind+idindSkip+8) + charShift]; ^ sortSuffixesBucket.cpp:86:44: warning: array subscript has type ‘char’ [-Wchar-subscripts] memcpy(ind1+charStart[c]indSkip, ind+idindSkip, indSkip); ^ sortSuffixesBucket.cpp:86:62: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] memcpy(ind1+charStart[c]indSkip, ind+idindSkip, indSkip); ^ sortSuffixesBucket.cpp:87:32: warning: array subscript has type ‘char’ [-Wchar-subscripts] charStart[c]++; ^ sortSuffixesBucket.cpp:89:36: warning: pointer of type ‘void ’ used in arithmetic [-Wpointer-arith] memcpy(ind+uB1[iu]indSkip, ind1+uB1[iu]indSkip, (uB2[iu]-uB1[iu])indSkip); ^ g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' funCompareUintAndSuffixesMemcmp.cpp funCompareUintAndSuffixesMemcmp.cpp: In function ‘int funCompareUintAndSuffixesMemcmp(const void, const void)’: funCompareUintAndSuffixesMemcmp.cpp:21:15: warning: unused variable ‘p5’ [-Wunused-variable] char p5=g_funCompareUintAndSuffixesMemcmp_G+va[1]+g_funCompareUintAndSuffixesMemcmp_L; ^ g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' TimeFunctions.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ErrorWarning.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' loadGTF.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' streamFuns.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' stringSubstituteAll.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Transcriptome.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Transcriptome_quantAlign.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_quantTranscriptome.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Quantifications.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Transcriptome_geneCountsAddAlign.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sjdbLoadFromFiles.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sjdbLoadFromStream.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sjdbPrepare.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sjdbBuildIndex.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' sjdbInsertJunctions.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' mapThreadsSpawn.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::cxx11::string, std::vector<std::cxx11::basic_string >)’: Parameters_readSAMheader.cpp:26:29: warning: ignoring return value of ‘int system(const char)’, declared with attribute warn_unused_result [-Wunused-result] system(com1.c_str()); ^ g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' BAMoutput.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' BAMfunctions.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' ReadAlign_alignBAM.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' BAMbinSortByCoordinate.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' signalFromBAM.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' bamRemoveDuplicates.cpp g++ -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp:5:78: warning: unused parameter ‘bgzfBAM’ [-Wunused-parameter] void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF bgzfBAM, Parameters P) { ^ g++ -c -O3 -pipe -Wall -Wextra bam_cat.c g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Feb 8 13:26:19 +06 2018 :/home/kibria/STAR/source"' SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Chain.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o sortSuffixesBucket.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o GlobalVariables.cpp -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:61:98: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(("ls -lL " + rfName + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ^ Parameters_openReadsFiles.cpp:33:20: warning: variable ‘imate’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Wclobbered] for (uint imate=0;imate<readFilesIn.size();imate++) {//open readIn files

That's it. Is this okay?

Thanks in advance, Kibria.

kibriadurlav commented 6 years ago

Update: Again running the make STAR command showed, make: 'STAR' is up to date. :dancing_men: @khllkcm

alexdobin commented 6 years ago

Hi Kibria,

it seems that it worked, just try to run it. Also, you can always try the pre-compiled executables, in the bin/ directory.

Cheers Alex

kibriadurlav commented 6 years ago

Hi @alexdobin

Thank you for your reply. Yes, STAR is working now. But I am getting an error like this,

./_STARtmp//readsCommand_read1: line 3: /dev/fd/63: Permission denied

Any idea? Sorry for being off topic.

alexdobin commented 6 years ago

Hi Kibria,

please post or e-mail me the Log.out file.

Cheers Alex

kibriadurlav commented 6 years ago

Hi Alex,

Thank you for your reply. I re-downloaded the ENCODE fastq file, and this time it came up without any error, could be file wasn't downloaded properly. Anyway, thanks for your help.

Cheers, Kibria.