Question: perl warning message

Question

[hafida.bioinfo.125]

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.

Answer 1

[Jeremy Leipzig]

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?

[hafida.bioinfo.125]

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

[Jeremy Leipzig]

the empty files are a possible culprit. is there anything special about K23?

[hafida.bioinfo.125]

anything special about K23, like what?

[Jeremy Leipzig]

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?

[hafida.bioinfo.125]

SOAP fails to assemble all the samples this is the problem.

[Jeremy Leipzig]

oh so K23 is kmer size 23? try running SOAPdenovo separately from EUPAN and post whatever errors you see as a new Biostar question

[hafida.bioinfo.125]

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

[Jeremy Leipzig]

is Bamtools installed?

[hafida.bioinfo.125]

yes it's istalled already

[Jeremy Leipzig]

make sure your LD_LIBRARY_PATH knows where to find it Trouble Compiling C++ Code With Bamtools