Unable to install Smufin on cluster

[ricch...@gmail.com]

Hello Authors,

I am using the version of gcc and openmpi as mentioned in the README file (Openmpi version 2.0.2, Gcc version 6.3.0) and not able to install smufin_v0.9.3. While executing the make command following error is reported:

Must remake target `SMuFin'.
Need a job token; we don't have children
mpic++ -o SMuFin main.cpp alphabet.o amino.o array8.o array.o direct.o genarray.o genhash.o gmem.o gs2k.o hash.o mathutil.o mystring.o parse.o seqgen.o stack.o stree.o trace.o util.o blind2.o deep2.o ds.o globals.o helped.o shallow.o getway_s asm bwa.a samtools.a -lz -lmpi -lgomp
Putting child 0x00666250 (SMuFin) PID 25973 on the chain.
Commands of `SMuFin' are being run.
Live child 0x00666250 (SMuFin) PID 25973
/tmp/cccOHGOZ.o: In function `process_det_mut_block(void*)':
main.cpp:(.text+0xd05): undefined reference to `gsuffixfilteraux(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, int> > >&, char*, unsigned long, char*, unsigned long, char*, unsigned long, std::vector<_SNV, std::allocator<_SNV> >*)'
blind2.o: In function `insert_suffix':
blind2.c:(.text+0x4d6): undefined reference to `new_node__blind_ssort'
blind2.c:(.text+0x59a): undefined reference to `new_node__blind_ssort'
deep2.o: In function `qs_unrolled_lcp':
deep2.c:(.text+0x267): undefined reference to `cmp_unrolled_lcp'
deep2.c:(.text+0x2dd): undefined reference to `cmp_unrolled_lcp'
helped.o: In function `split_group':
helped.c:(.text+0x147d): undefined reference to `vecswap2'
helped.c:(.text+0x14de): undefined reference to `vecswap2'
shallow.o: In function `shallow_mkq':
shallow.c:(.text+0x19c): undefined reference to `med3func'
shallow.c:(.text+0x1e2): undefined reference to `med3func'
shallow.c:(.text+0x227): undefined reference to `med3func'
shallow.c:(.text+0x243): undefined reference to `med3func'
shallow.c:(.text+0x46a): undefined reference to `vecswap2'
shallow.c:(.text+0x4c8): undefined reference to `vecswap2'
shallow.o: In function `shallow_mkq16':
shallow.c:(.text+0x6c6): undefined reference to `med3func'
shallow.c:(.text+0x70c): undefined reference to `med3func'
shallow.c:(.text+0x751): undefined reference to `med3func'
shallow.c:(.text+0x76d): undefined reference to `med3func'
shallow.c:(.text+0xa00): undefined reference to `vecswap2'
shallow.c:(.text+0xa5e): undefined reference to `vecswap2'
shallow.o: In function `shallow_mkq32':
shallow.c:(.text+0xc5c): undefined reference to `med3func'
shallow.c:(.text+0xca2): undefined reference to `med3func'
shallow.c:(.text+0xce7): undefined reference to `med3func'
shallow.c:(.text+0xd03): undefined reference to `med3func'
shallow.c:(.text+0x1050): undefined reference to `vecswap2'
shallow.c:(.text+0x10ae): undefined reference to `vecswap2'
shallow.o: In function `shallow_inssort_lcp':
shallow.c:(.text+0x12d0): undefined reference to `cmp_unrolled_shallow_lcp'
collect2: error: ld returned 1 exit status
Reaping losing child 0x00666250 PID 25973
make: *** [SMuFin] Error 1
Removing child 0x00666250 PID 25973 from chain.

Can you please suggest why such an error is reported?

Thanks

[SMuFin]

Hello,

How many threads are you using?

Best Regards

[ricch...@gmail.com]

Hello,

I was able to install smufin using openmpi version 1.5.5, gcc version 4.8.5.
But now I am getting following error while running smufin on my data:
Checking input data files...
BWT index found for /puppy/scratch/SimRic/hg19_SORTED.fa
num_targets: 84
100 ;@CFFFF*GHHHchr3-48479674
Parse error at line 1965: sequence and quality are inconsistent
*** Process received signal ***
Signal: Aborted (6)
Signal code: (-6)
/lib64/libpthread.so.0(+0xf850) [0x7f6145d59850]
/lib64/libc.so.6(gsignal+0x35) [0x7f61459f4875]
/lib64/libc.so.6(abort+0x181) [0x7f61459f5e51]
/smufin_0.9.3_mpi_beta/SMuFin() [0x547521]
smufin_0.9.3_mpi_beta/SMuFin(sam_read1+0xbfa) [0x54896b]
smufin_0.9.3_mpi_beta/SMuFin(samread+0x70) [0x534100]
smufin_0.9.3_mpi_beta/SMuFin(main_samview+0x4c8) [0x532993]
smufin_0.9.3_mpi_beta/SMuFin(gsuffix_co_asm_impl+0x25) [0x491b5d]
smufin_0.9.3_mpi_beta/SMuFin(gsuffix_co+0x2b) [0x488ed5]
smufin_0.9.3_mpi_beta/SMuFin(_Z18process_block_funcPv+0x94) [0x4705d2]
lib64/libpthread.so.0(+0x7806) [0x7f6145d51806]
lib64/libc.so.6(clone+0x6d) [0x7f6145aa067d]
*** End of error message ***

Can you please suggest what could be the reason for error?

I am giving following command to run smufin:
sbatch --mem=130G -n 30 -N 2 --wrap="mpirun --np 3 smufin_0.9.3_mpi_beta/SMuFin --ref hg19_SORTED.fa --normal_fastq_1 normal_fastqs_1.txt --normal_fastq_2 normal_fastqs_2.txt --tumor_fastq_1 tumor_fastqs_1.txt --tumor
_fastq_2 tumor_fastqs_2.txt --cpus_per_node 10"

Thanks

[edev...@gmail.com]

I had similar problem with smufin, due to the fact that we host centralised bwa index that are non writable for  users

smufin in main.cpp check for index readable AND writable.
see

char* str_buff = (char*)malloc(FILENAME_MAX);
        strcpy(str_buff, ref_file);
        strcat(str_buff, ".bwt");
        if (access(str_buff, R_OK | W_OK))
                gen_bwt_index = 1;
        strcpy(str_buff, ref_file);
        strcat(str_buff, ".amb");
        if (access(str_buff, R_OK | W_OK))
                gen_bwt_index = 1;
        strcpy(str_buff, ref_file);
        strcat(str_buff, ".ann");
        if (access(str_buff, R_OK | W_OK))
                gen_bwt_index = 1;
        strcpy(str_buff, ref_file);
        strcat(str_buff, ".pac");
        if (access(str_buff, R_OK | W_OK))
                gen_bwt_index = 1;
        strcpy(str_buff, ref_file);
        strcat(str_buff, ".sa");
        if (access(str_buff, R_OK | W_OK))
                gen_bwt_index = 1;

patching main.cpp to just check for R_OK indexes solved the problem

regards

Eric