dear friends,
I need a help, i tried to use EUPAN-v0.44.
when i execute this command line : eupan assemble soapdenovo -t 4 -k 23 -g data/ assembly_soap/ /home/hp/Bureau/SOAPdenovo2-src-r240
after runing it gives me this:
Process sample data/sampleA/ ...
Use of uninitialized value $seq in split at /home/hp/Bureau/EUPAN-v0.44/lib/EUPANassem.pm line 231.
Process sample data/sampleC/ ...
Use of uninitialized value $seq in split at /home/hp/Bureau/EUPAN-v0.44/lib/EUPANassem.pm line 231.
Process sample data/sampleB/ ...
Use of uninitialized value $seq in split at /home/hp/Bureau/EUPAN-v0.44/lib/EUPANassem.pm line 231.**
I use perl-5.32.1 can you help me please to solve this problem. thank you for advance.
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written
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hafida.bioinfo.125 •
I imagine SOAPdenovo either crashed or just didn't produce a scaffold file. Can you make sure all the files in your output directory (assembly_soap) are not empty? What does tree -s assembly_soap look like?
in the assembly_soap i have 3 sub-directories, in each one i have 5 files, the K23.cgContig and K23.cgScaffold files are empty.
after runing tree -s assembly_soap, i get this:
root@hp-HP-ProBook-640-G1:~# tree -s assembly_soap
assembly_soap [error opening dir]
0 directories, 0 files
the empty files are a possible culprit. is there anything special about K23?
anything special about K23, like what?
is there any reason why SOAP would fail to assemble that particular sample? are the files bigger, or corrupt? if you remove that sample altogether does EUPAN finish its pipeline?
SOAP fails to assemble all the samples this is the problem.
oh so K23 is kmer size 23? try running SOAPdenovo separately from EUPAN and post whatever errors you see as a new Biostar question
i re-installed EUPAN, and when i type make it gives me this error:
root @ hp-HP-ProBook-640-G1: ~ / Desktop / EUPAN-v0.44 # make
make [1]: we enter the directory "/home/hp/Bureau/EUPAN-v0.44/src/bam2cov"
g ++ -O2 -o ../../bin/bam2cov bam2cov.cpp -lbamtools -L ../../lib/ -I ../../lib/include/
/tmp/cc91DQLe.o: In the "main" function:
bam2cov.cpp :(. text.startup + 0xad): undefined reference to "BamTools :: BamReader :: Open (std :: __ cxx11 :: basic_string <char, std :: char_traits <char>, std :: allocator <char> > const &) "
collect2: error: ld returned 1 exit status
Makefile: 2: the recipe for the target "../../bin/bam2cov" failed
make [1]: *** [../../bin/bam2cov] Error 1
make [1]: we leave the directory "/home/hp/Bureau/EUPAN-v0.44/src/bam2cov"
make [1]: we enter the directory "/home/hp/Bureau/EUPAN-v0.44/src/ccov"
g ++ -O2 -o ../../bin/ccov CCOV.cpp GTF.cpp -lz -lbamtools -L ../../lib/ -I ../../lib/include/
/tmp/cch74WTW.o: In the "main" function:
CCOV.cpp :(. Text.startup + 0x1cb): undefined reference to "BamTools :: BamReader :: Open (std :: __ cxx11 ::
basic_string <char, std :: char_traits <char>, std :: allocator <char> > const &) "
collect2: error: ld returned 1 exit status
Makefile: 2: the recipe for the target "../../bin/ccov" failed
make [1]: *** [../../bin/ccov] Error 1
make [1]: we leave the directory "/home/hp/Bureau/EUPAN-v0.44/src/ccov"
Makefile: 5: the recipe for target "all" failed
make: *** [all] Error 2
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written
by
hafida.bioinfo.125 •
is Bamtools installed?
yes it's istalled already
make sure your LD_LIBRARY_PATH knows where to find it Trouble Compiling C++ Code With Bamtools
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