[Thorondor]

hmmm, never got a error like that.

you have velvet 1.1.03 and oases 0.1.20 ?

[Jenzo]

Right, I downloaded them a few hours ago..

Here's the complete output:

jpreuss@velvet-vm:~/Oases$ make 'VELVET_DIR=/home/jpreuss/Velvet' 'MAXKMERLENGTH=35'
rm -f obj/*.o obj/dbg/*.o 
cd /home/jpreuss/Velvet && make obj
make[1]: Betrete Verzeichnis '/home/jpreuss/Velvet'
cd third-party/zlib-1.2.3; ./configure; make; rm minigzip.o; rm example.o
Checking for gcc...
Building static library libz.a version 1.2.3 with gcc.
Checking for unistd.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for errno.h... Yes.
Checking for mmap support... Yes.
make[2]: Betrete Verzeichnis '/home/jpreuss/Velvet/third-party/zlib-1.2.3'
gcc -O3 -DUSE_MMAP   -c -o example.o example.c
gcc -O3 -DUSE_MMAP   -c -o adler32.o adler32.c
gcc -O3 -DUSE_MMAP   -c -o compress.o compress.c
gcc -O3 -DUSE_MMAP   -c -o crc32.o crc32.c
gcc -O3 -DUSE_MMAP   -c -o gzio.o gzio.c
gcc -O3 -DUSE_MMAP   -c -o uncompr.o uncompr.c
gcc -O3 -DUSE_MMAP   -c -o deflate.o deflate.c
gcc -O3 -DUSE_MMAP   -c -o trees.o trees.c
gcc -O3 -DUSE_MMAP   -c -o zutil.o zutil.c
gcc -O3 -DUSE_MMAP   -c -o inflate.o inflate.c
gcc -O3 -DUSE_MMAP   -c -o infback.o infback.c
gcc -O3 -DUSE_MMAP   -c -o inftrees.o inftrees.c
gcc -O3 -DUSE_MMAP   -c -o inffast.o inffast.c
ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 
gcc -O3 -DUSE_MMAP -o example example.o -L. libz.a
gcc -O3 -DUSE_MMAP   -c -o minigzip.o minigzip.c
gcc -O3 -DUSE_MMAP -o minigzip minigzip.o -L. libz.a
make[2]: Verlasse Verzeichnis '/home/jpreuss/Velvet/third-party/zlib-1.2.3'
rm obj/*.o obj/dbg/*.o 
rm: Entfernen von „obj/dbg/*.o“ nicht möglich: Datei oder Verzeichnis nicht gefunden
make[1]: [cleanobj] Fehler 1 (ignoriert)
mkdir -p obj
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
src/run.c: In function ‘main’:
src/run.c:212: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o 
src/splayTable.c: In function ‘computeClearHSPs’:
src/splayTable.c:631: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:931: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o 
make[1]: Verlasse Verzeichnis '/home/jpreuss/Velvet'
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/oases.c -o obj/oases.o -I/home/jpreuss/Velvet/src
gcc -Wall -O3 -D MAXKMERLENGTH=35 -D CATEGORIES=2 -c src/transcript.c -o obj/transcript.o -I/home/jpreuss/Velvet/src
src/transcript.c:564: error: static declaration of ‘getTotalCoverage’ follows non-static declaration
/home/jpreuss/Velvet/src/graph.h:99: note: previous declaration of ‘getTotalCoverage’ was here
make: *** [obj/transcript.o] Fehler 1

[Thorondor]

okey. can't help here. :-/

Anyway you should try to ask for help over the oases mailing list: http://listserver.ebi.ac.uk/mailman/...fo/oases-users

zerbino is also active there and normally answers fast.

[Jenzo]

Thanks a lot. I will try to get an answer there :-) SOLVED:

Hey!
I got an answer via the Oases mailing list. The problem is, according to Sylvain Foret, that 'getTotalCoverage' was made public in Velvet 1.1.03, but not changed in Oases. One can use Velvet 1.1.02 instead or comment out the definition of 'getTotalCoverage' in transcript.c.
It is suggested that Oases will be fixed.

[chrisbala]

Hi everyone,

I'm using OASES for the first time.

Quick question:
Should I expect anything to be printed to output while OASES is running? (aka immediately after I start the program)

It seems to be running but nothing has been printed and I would love to get some feel good progress report... (to make sure something is actually happening in there!)

thanks!

[chrisbala]

answer received: I got some output after a few minutes. Looks like things are going...

[Thorondor]

depending on your number of reads it takes "hours" till it finishes.

5hours
30GB RAM
with around 70.000.0000 reads with average length 90

you can speed things up with the new parallel mode but didn't tried that out yet.

[oliviera]

dear Jenzo, dear All,

I have the same problem than you Jenzo: Oases crashes with the same error that you describe. I guess it is better to use the last release of velvet. Have you managed to use the last release or did you go back to the 1.1.02?
Thanx
Olivier

[Jenzo]

Dear Olivier,
I'm using Velvet 1.1.03 with Oases 0.1.21. It works perfect now..
Perhaps you try to get the latest version of both, recompile and run it again, it should work then :-)
Greets,
Jenzo

[oliviera]

Thanx for your fast reply,
I download and install without problem velvet 1.1.03 with
make 'MAXKMERLENGTH=57' 'BIGASSEMBLY=1' 'OPENMP=1'

By ther way I have 76bp paired end reads so I thought it is interesting to use MAXKMERLENGTH=57. Is it right ?

I then tried to install the last release oases 0.1.21 with
make 'VELVET_DIR=/data/shared/src/velvet/velvet_1.1.03/' 'MAXKMERLENGTH=57' 'BIGASSEMBLY=1' 'OPENMP=1'
This is not working.
When I remove the option 'OPENMP=1' (I thought to use it to turn on the multithread processing) then installation goes until the end.
So I guess their is something wrong with Oases and the multithread support. Or I do something wrong

[Thorondor]

on the oases malinglist Daniel Zerbino wrote:
"Are you compiling Oases with the OPENMP flag? This indeed is not allowed
by the Oases Makefile, as Oases will not be accelerated by the parallel
sections of Velvet (since they are Velvet specific)."

feel free to add to the oases mailinglist:

http://listserver.ebi.ac.uk/mailman/listinfo/oases-users

[Apexy]

Hi Oliviera,
Please pardon my ignorance and it this respond is coming late as I started using oases only recently. I wonder if there is a multi-threaded version of oases implementing openmpi at this stage. I looked at the README.txt and did not see openmpi at compilation. If there is some documentation relating to oases and openmpi, I would very much cherish you refer me to. It could be the reason while compilation is unsuccessful with 'OPENMP=1' argument

[Apexy]

Oops! I noticed Thorondor gave a respond already

[catfisher]

Hi, Brett
Have you figured out the problem that Oases inserts Ns and possible ways to avoid them? I encountered the same problem, and I saw that there is an option for scaffolding in Oases, I set it as 'no', but still got contigs with a lot of N's inserted in them. Not sure if you have figured out this problem, or someone else did, thanks

[Thorondor]

yup, this happens also for me, scaffolding is off per default in oases and but you still get this Ns because oases still connect read pairs.

zerbino wrote over oases mailinglist:
"scaffolding only means that you allow Velvet/Oases to take a leap of
faith. Paired-end information is always used in Oases (when available,
of course)."