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Old 08-16-2019, 11:25 AM   #8
guineverelee
Junior Member
 
Location: USA

Join Date: Aug 2019
Posts: 5
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Hi GenoMax and all

I am unable to re-define my velveth MAXKMERLENGTH. It is currently at default 31. Please see error message below. Any clue what's going on? Thanks again!!

$ cd ./Velvet_1.2.10
$ make ’MAXKMERLENGTH=150’
rm obj/*.o obj/dbg/*.o
rm: obj/dbg/*.o: No such file or directory
make: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o
In file included from src/run.c:31:
In file included from src/run.h:35:
src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here,
followed by #define of a different macro [-Wheader-guard]
#ifndef _SSCAFFOLD_H_
^~~~~~~~~~~~~
src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean
'_SSCAFFOLD_H_'?
#define _SCAFFOLD_H_
^~~~~~~~~~~~
_SSCAFFOLD_H_
1 warning generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o
In file included from src/run2.c:26:
In file included from src/run.h:35:
src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here,
followed by #define of a different macro [-Wheader-guard]
#ifndef _SSCAFFOLD_H_
^~~~~~~~~~~~~
src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean
'_SSCAFFOLD_H_'?
#define _SCAFFOLD_H_
^~~~~~~~~~~~
_SSCAFFOLD_H_
1 warning generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o
In file included from src/concatenatedGraph.c:25:
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
^
src/concatenatedGraph.c:56:14: note: used here
position = getShortReadMarkerPosition(marker);
^
In file included from src/concatenatedGraph.c:25:
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
^
src/concatenatedGraph.c:59:4: note: used here
setShortReadMarkerPosition(marker, position);
^
2 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o
src/passageMarker.c:50:1: warning: unused function 'PM_I2P' [-Wunused-function]
DECLARE_FAST_ACCESSORS (PM, PassageMarker, markerMemory)
^
src/allocArray.h:69:21: note: expanded from macro 'DECLARE_FAST_ACCESSORS'
static inline type* name##_I2P(ArrayIdx idx) \
^
<scratch space>:412:1: note: expanded from here
PM_I2P
^
1 warning generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o
src/graphStats.c:1961:69: warning: format specifies type 'long' but the argument
has type 'long long' [-Wformat]
..."PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
~~~ ^~~~~~~~~~~~~~~~~~~~~~
%lld
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^~~~~~~~~~~
In file included from src/graphStats.c:28:
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
^
src/graphStats.c:848:19: note: used here
starts[index] = getShortReadMarkerPosition(marker);
^
In file included from src/graphStats.c:28:
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' is not
defined [-Wundefined-inline]
extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
^
src/graphStats.c:849:34: note: used here
stops[index] = starts[index] - getShortReadMarkerOffset(...
^
3 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o
In file included from src/correctedGraph.c:26:
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
^
src/correctedGraph.c:776:15: note: used here
position = getShortReadMarkerPosition(shortMarker);
^
In file included from src/correctedGraph.c:26:
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
^
src/correctedGraph.c:799:4: note: used here
setShortReadMarkerPosition(shortMarker, position);
^
2 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o
src/readSet.c:641:21: warning: incompatible pointer types assigning to 'gzFile'
(aka 'struct gzFile_s *') from 'AutoFile *' [-Wincompatible-pointer-types]
file.gzFile = file.autoFile = NULL;
^ ~~~~~~~~~~~~~~~~~~~~
src/readSet.c:680:22: warning: incompatible pointer types assigning to 'gzFile'
(aka 'struct gzFile_s *') from 'AutoFile *' [-Wincompatible-pointer-types]
file1.gzFile = file1.autoFile = NULL;
^ ~~~~~~~~~~~~~~~~~~~~~
src/readSet.c:681:22: warning: incompatible pointer types assigning to 'gzFile'
(aka 'struct gzFile_s *') from 'AutoFile *' [-Wincompatible-pointer-types]
file2.gzFile = file2.autoFile = NULL;
^ ~~~~~~~~~~~~~~~~~~~~~
src/readSet.c:632:1: warning: unused function 'kseq_rewind' [-Wunused-function]
KSEQ_INIT(FileGZOrAuto, fileGZOrAuto_read)
^
src/kseq.h:220:2: note: expanded from macro 'KSEQ_INIT'
__KSEQ_BASIC(type_t) \
^
src/kseq.h:152:21: note: expanded from macro '__KSEQ_BASIC'
static inline void kseq_rewind(kseq_t *ks...
^
4 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o
src/binarySequences.c:304:69: warning: format specifies type 'unsigned long' but
the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
...location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_...
~~~ ^~~~~~~~~~~~~~
%llx
src/binarySequences.c:304:85: warning: format specifies type 'long' but the
argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
...seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (...
~~~ ^~~~~~~~~~~~~~~~~~~~~~~~
%llu
src/binarySequences.c:304:111: warning: format specifies type 'unsigned long'
but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
...0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
~~~ ^~~~~~~~~~~~~~~~~~~
%llx
src/binarySequences.c:389:45: warning: format specifies type 'long' but the
argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
~~~ ^~~~~~
%llu
4 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
In file included from src/shortReadPairs.c:34:
src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here,
followed by #define of a different macro [-Wheader-guard]
#ifndef _SSCAFFOLD_H_
^~~~~~~~~~~~~
src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean
'_SSCAFFOLD_H_'?
#define _SCAFFOLD_H_
^~~~~~~~~~~~
_SSCAFFOLD_H_
In file included from src/shortReadPairs.c:27:
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
^
src/shortReadPairs.c:590:14: note: used here
position = getShortReadMarkerPosition(marker);
^
In file included from src/shortReadPairs.c:27:
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
^
src/shortReadPairs.c:593:4: note: used here
setShortReadMarkerPosition(marker, position);
^
3 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o
src/graphReConstruction.c:1407:65: warning: format specifies type 'long' but the
argument has type '__darwin_suseconds_t' (aka 'int') [-Wformat]
...=== Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec);
~~~~~ ^~~~~~~~~~~~
%06d
src/graphReConstruction.c:1436:59: warning: format specifies type 'long' but the
argument has type '__darwin_suseconds_t' (aka 'int') [-Wformat]
velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec);
~~~~~ ^~~~~~~~~~~~
%06d
2 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o
In file included from src/preGraph.c:35:
In file included from src/run.h:35:
src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here,
followed by #define of a different macro [-Wheader-guard]
#ifndef _SSCAFFOLD_H_
^~~~~~~~~~~~~
src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean
'_SSCAFFOLD_H_'?
#define _SCAFFOLD_H_
^~~~~~~~~~~~
_SSCAFFOLD_H_
src/preGraph.c:165:17: warning: taking address of packed member 'preArcRight' of
class or structure 'preNode_st' may result in an unaligned pointer value
[-Waddress-of-packed-member]
preArcPtr = &(preNode->preArcRight);
^~~~~~~~~~~~~~~~~~~~
src/preGraph.c:167:17: warning: taking address of packed member 'preArcLeft' of
class or structure 'preNode_st' may result in an unaligned pointer value
[-Waddress-of-packed-member]
preArcPtr = &(preNode->preArcLeft);
^~~~~~~~~~~~~~~~~~~
src/preGraph.c:285:17: warning: taking address of packed member 'preArcRight' of
class or structure 'preNode_st' may result in an unaligned pointer value
[-Waddress-of-packed-member]
preArcPtr = &(preNode->preArcRight);
^~~~~~~~~~~~~~~~~~~~
src/preGraph.c:287:17: warning: taking address of packed member 'preArcLeft' of
class or structure 'preNode_st' may result in an unaligned pointer value
[-Waddress-of-packed-member]
preArcPtr = &(preNode->preArcLeft);
^~~~~~~~~~~~~~~~~~~
src/preGraph.c:520:27: warning: unused function 'mergeDescriptors_pg'
[-Wunused-function]
static inline Descriptor *mergeDescriptors_pg(Descriptor * descr,
^
src/preGraph.c:635:27: warning: unused function 'mergeDescriptorsH2H_pg'
[-Wunused-function]
static inline Descriptor *mergeDescriptorsH2H_pg(Descriptor * descr,
^
src/preGraph.c:760:27: warning: unused function 'mergeDescriptorsF2F_pg'
[-Wunused-function]
static inline Descriptor *mergeDescriptorsF2F_pg(Descriptor * descr,
^
8 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
src/preGraphConstruction.c:525:58: warning: format specifies type 'long' but the
argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
...velvetLog("readIndex %ld beyond string len %ld\n", (uint64_t) readIndex...
~~~ ^~~~~~~~~~~~~~~~~~~~
%llu
src/preGraphConstruction.c:525:80: warning: format specifies type 'long' but the
argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
...string len %ld\n", (uint64_t) readIndex, (uint64_t) tString->length);
~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~
%llu
2 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o
In file included from src/readCoherentGraph.c:25:
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
^
src/readCoherentGraph.c:367:14: note: used here
position = getShortReadMarkerPosition(marker);
^
In file included from src/readCoherentGraph.c:25:
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
^
src/readCoherentGraph.c:369:3: note: used here
setShortReadMarkerPosition(marker, position);
^
2 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o
src/kmer.c:28:23: warning: unused variable 'longLongLeftFilter'
[-Wunused-const-variable]
static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62;
^
src/kmer.c:29:23: warning: unused variable 'longLeftFilter'
[-Wunused-const-variable]
static const uint32_t longLeftFilter = (uint32_t) 3 << 30;
^
src/kmer.c:30:23: warning: unused variable 'intLeftFilter'
[-Wunused-const-variable]
static const uint16_t intLeftFilter = (uint16_t) 3 << 14;
^
src/kmer.c:31:22: warning: unused variable 'charLeftFilter'
[-Wunused-const-variable]
static const uint8_t charLeftFilter = (uint8_t) 3 << 6;
^
4 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o
In file included from src/scaffold.c:39:
src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here,
followed by #define of a different macro [-Wheader-guard]
#ifndef _SSCAFFOLD_H_
^~~~~~~~~~~~~
src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean
'_SSCAFFOLD_H_'?
#define _SCAFFOLD_H_
^~~~~~~~~~~~
_SSCAFFOLD_H_
In file included from src/scaffold.c:32:
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not
defined [-Wundefined-inline]
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
^
src/scaffold.c:455:7: note: used here
getShortReadMarkerPosition(shortMarker);
^
In file included from src/scaffold.c:32:
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' is not
defined [-Wundefined-inline]
extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
^
src/scaffold.c:457:7: note: used here
getShortReadMarkerOffset(shortMarker);
^
3 warnings generated.
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o
src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier
[-Wduplicate-decl-specifier]
static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzi...
^
1 warning generated.
gcc -Wall -m64 -O3 -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm
gcc -Wall -m64 -O3 -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm
Guineveres-MacBook-Pro:Velvet_1.2.10 guin$
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