Question: Error in velvet
0
gravatar for suhalsuhaimi
3.9 years ago by
suhalsuhaimi30
United States
suhalsuhaimi30 wrote:

Hi,

I have a problem while try to run 'make velveth' and 'make velvetg' but I don't know how to fix it.  I'm using Ubuntu in VM

When I type this command:

make velveth

The error come up like this:

rm obj/*.o obj/dbg/*.o
rm: cannot remove ‘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
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
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1060:14: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
      RefInfo refElem;
              ^
src/splayTable.c: In function ‘scanReferenceSequences’:
src/splayTable.c:877:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c: In function ‘scanBinaryReferenceSequences’:
src/splayTable.c:933:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c:949:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAXLINE, file);
         ^
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1207:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
src/splayTable.c:1213:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
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
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
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o
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: In function ‘readFastXFile’:
src/readSet.c:641:21: warning: assignment from incompatible pointer type [enabled by default]
         file.gzFile = file.autoFile = NULL;
                     ^
src/readSet.c: In function ‘readFastXPair’:
src/readSet.c:680:22: warning: assignment from incompatible pointer type [enabled by default]
         file1.gzFile = file1.autoFile = NULL;
                      ^
src/readSet.c:681:22: warning: assignment from incompatible pointer type [enabled by default]
         file2.gzFile = file2.autoFile = NULL;
                      ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o
src/binarySequences.c: In function ‘importCnyReadSet’:
src/binarySequences.c:314:12: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
    RefInfo refElem;
            ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
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
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
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
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
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
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o
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: In function ‘pcloseNoStderr’:
src/autoOpen.c:49:6: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
  int rc, status;
      ^
src/autoOpen.c: In function ‘popenNoStderr’:
src/autoOpen.c:28:6: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result [-Wunused-result]
   dup(out[1]);
      ^

Please help me.

 

velvet • 1.1k views
ADD COMMENTlink modified 3.9 years ago by John Marshall1.6k • written 3.9 years ago by suhalsuhaimi30
0
gravatar for John Marshall
3.9 years ago by
John Marshall1.6k
Glasgow, Scotland
John Marshall1.6k wrote:

These are all warnings, and can be mostly safely ignored.  Unless there are some other messages on the end that you haven't shown us, you have in fact built working velvetg and velveth executables.

Are there any messages after the part that builds the executables themselves?  Namely after

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
ADD COMMENTlink written 3.9 years ago by John Marshall1.6k

there is no other messages after that.

Yes, i try to execute velveth and velvetg. but there is still have an error. how to fix it. can you teach me?

ADD REPLYlink written 3.9 years ago by suhalsuhaimi30

I tyr to execute velveth and velvetg again, and it appear like this:

make velveth velvetg
rm obj/*.o obj/dbg/*.o
rm: cannot remove ‘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
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
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1060:14: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
      RefInfo refElem;
              ^
src/splayTable.c: In function ‘scanReferenceSequences’:
src/splayTable.c:877:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c: In function ‘scanBinaryReferenceSequences’:
src/splayTable.c:933:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c:949:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAXLINE, file);
         ^
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1207:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
src/splayTable.c:1213:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
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
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
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o
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: In function ‘readFastXFile’:
src/readSet.c:641:21: warning: assignment from incompatible pointer type [enabled by default]
         file.gzFile = file.autoFile = NULL;
                     ^
src/readSet.c: In function ‘readFastXPair’:
src/readSet.c:680:22: warning: assignment from incompatible pointer type [enabled by default]
         file1.gzFile = file1.autoFile = NULL;
                      ^
src/readSet.c:681:22: warning: assignment from incompatible pointer type [enabled by default]
         file2.gzFile = file2.autoFile = NULL;
                      ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o
src/binarySequences.c: In function ‘importCnyReadSet’:
src/binarySequences.c:314:12: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
    RefInfo refElem;
            ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
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
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
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
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
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
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o
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: In function ‘pcloseNoStderr’:
src/autoOpen.c:49:6: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
  int rc, status;
      ^
src/autoOpen.c: In function ‘popenNoStderr’:
src/autoOpen.c:28:6: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result [-Wunused-result]
   dup(out[1]);
      ^
make: `velvetg' is up to date.

 

And I also try to run this command:

velveth run31 31 -fastq.gz -short 1.fastq.gz 2.fastq.gz

 

Then it appear like this:

[0.000000] Reading FastQ file ERR351267_1.fastq.gz;
[47.787195] 1554894 sequences found
[47.787239] Done
[47.812862] Reading FastQ file ERR351267_2.fastq.gz;
[105.184772] 1554894 sequences found
[105.184826] Done
[105.233031] Reading read set file run31/Sequences;
[114.645745] 3109788 sequences found
[477.422910] Done
[477.507589] 3109788 sequences in total.
[477.830547] Writing into roadmap file run31/Roadmaps...
Killed

The 'Roadmaps' file is appear. I also try to run this command:

velvetg run31 -clean yes -exp_cov 21 -cov_cutoff 2.81 -min_contig_lgth 200

Error appear like this:
[0.000000] Reading roadmap file run31/Roadmaps
velvetg: run31/Roadmaps incomplete.: No such file or directory

how to fix the error. mybe im wrong from the beginning.

ADD REPLYlink written 3.9 years ago by suhalsuhaimi30

"Killed"

It is possible that your job is getting killed by the OS after reaching some sort of limit. Are you executing this job under a job scheduler?

ADD REPLYlink written 3.9 years ago by genomax69k

I would recommend running the sample files provided with the installation. You can find the test runs at the start of the manual, along with expected results. If those complete successfully, your problems are OS-related rather than velvet-related.

ADD REPLYlink written 3.9 years ago by Adrian Pelin2.3k
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