missing bwa executable after installation

[mathias....@gmail.com]

Hi,

I've problems installing the OpEx pipeline. As the manual suggests I downloaded and unpacked the OpEx-1.0.0.tar.gz and the genome human_g1k_v37.fasta (and the index file). Then I navigated into the resulting directory and executed the install.py script directing it to the geneome fasta file. It gave me a lot of warnings but no errors.

I continued to run the test_installation.py script which put out the following messeage:

================================================================================
Checking OpEx installation ... - Done.
OpEx is not installed correctly.
================================================================================

 I explored the subdirektories and found a log file in the folger _testinstall

13.11.2016 11:16:03 : Pipeline started
13.11.2016 11:16:03 : Mapping reads, converting output to BAM file, sorting and indexing BAM
13.11.2016 11:16:48 : Comparing number of reads in FASTQ and BAM files
13.11.2016 11:16:48 : test.bam does not exist, cannot proceed. OpEx run terminated

In the same directory is a file called test_opex_pipeline.sh which i ran, resulting in an error messeage telling me that the bwa executable is not in place.
Having a look into tools/bwa0.5.10 I realized it is really lacking a bwa binary. Making it by myself failed even though I have recently compiled another bwa version (something like 0.7) without any problems.

Would it be possible to direct OpEx to bwa version which is already running?

Best,
Mathias

[Márton Münz]

Dear Mathias,

It indeed seems that while BWA 0.5.10 has been successfully downloaded by your OpEx installer, the BWA package was not building properly on your machine.

Could you please send me the error message BWA gives you when you try to build it manually?

Yes, it is possible to try to use that pre-built version of bwa which is running well for you. While unlikely to have a major effect on the results, we cannot guarantee the same accuracy reported in the paper for versions of software which are not the standard OpEx versions. If you would still like to proceed with a non-standard version, you will have to hack the code a little bit:

You only have to edit the opex_pipeline_template file in the templates/ directory.

Find the line which starts as

"$opexdir/tools/stampy-1.0.14.1/stampy.py --bwa=$opexdir/tools/bwa-0.5.10/bwa ..."

and replace "--bwa=$opexdir/tools/bwa-0.5.10/bwa" with "--bwa=path/to/bwa/bwa" pointing to the appropriate bwa binary you'd like to use.

This should work. If bwa was the only problem, and the version of bwa you use is compatible with stampy, the test_installation.py script should now give you positive result. Let me know!

But in any case, please can you send me the bwa 0.5.10 building error messages as it would be good to know what went wrong there and the best would be to fix that problem.

Best,

Márton

[mathias....@gmail.com]

Hi Márto,

I downloaded bwa 0.5.10 again and tried to build it again. Here's the error messeage:

pogopanther@Stein:~/Downloads/bwa-0.5.10$ make
^[[3~make[1]: Verzeichnis „/home/pogopanther/Downloads/bwa-0.5.10“ wird betreten
make[1]: Für das Ziel „lib“ ist nichts zu tun.
make[1]: Verzeichnis „/home/pogopanther/Downloads/bwa-0.5.10“ wird verlassen
make[1]: Verzeichnis „/home/pogopanther/Downloads/bwa-0.5.10/bwt_gen“ wird betreten
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:824:15: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
  unsigned int oldInverseSa0RelativeRank = 0;
               ^
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:899:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
  unsigned int bitsInWordMinusBitPerChar;
               ^
bwt_gen.c: In function ‘BWTIncConstructFromPacked’:
bwt_gen.c:1416:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&lastByteLength, sizeof(unsigned char), 1, packedFile);
  ^
bwt_gen.c:1432:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile);
  ^
bwt_gen.c:1447:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile);
   ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   QSufSort.c -o QSufSort.o
QSufSort.c: In function ‘QSufSortSuffixSort’:
QSufSort.c:89:6: warning: variable ‘maxNumInputSymbol’ set but not used [-Wunused-but-set-variable]
  int maxNumInputSymbol;
      ^
ar -scru libbwtgen.a bwt_gen.o QSufSort.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Verzeichnis „/home/pogopanther/Downloads/bwa-0.5.10/bwt_gen“ wird verlassen
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   utils.c -o utils.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwt.c -o bwt.o
bwt.c:147:8: warning: ‘__occ_aux’ is static but used in inline function ‘bwt_2occ’ which is not static
   m += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~l&31)<<1)) - 1), c);
        ^
bwt.c:146:9: warning: ‘__occ_aux’ is static but used in inline function ‘bwt_2occ’ which is not static
    m += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
         ^
bwt.c:140:8: warning: ‘__occ_aux’ is static but used in inline function ‘bwt_2occ’ which is not static
   n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
        ^
bwt.c:138:9: warning: ‘__occ_aux’ is static but used in inline function ‘bwt_2occ’ which is not static
    n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
         ^
bwt.c:109:7: warning: ‘__occ_aux’ is static but used in inline function ‘bwt_occ’ which is not static
  n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
       ^
bwt.c:106:8: warning: ‘__occ_aux’ is static but used in inline function ‘bwt_occ’ which is not static
   n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
        ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtio.c -o bwtio.o
In file included from bwtio.c:4:0:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
bwtio.c: In function ‘bwt_restore_sa’:
bwtio.c:36:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&primary, sizeof(bwtint_t), 1, fp);
  ^
bwtio.c:38:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(skipped, sizeof(bwtint_t), 4, fp); // skip
  ^
bwtio.c:39:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
  ^
bwtio.c:40:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&primary, sizeof(bwtint_t), 1, fp);
  ^
bwtio.c:47:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
  ^
bwtio.c: In function ‘bwt_restore_bwt’:
bwtio.c:62:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
  ^
bwtio.c:63:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
  ^
bwtio.c:64:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(bwt->bwt, 4, bwt->bwt_size, fp);
  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtaln.c -o bwtaln.o
In file included from bwtaln.h:5:0,
                 from bwtaln.c:11:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtgap.c -o bwtgap.o
In file included from bwtgap.h:4:0,
                 from bwtgap.c:4:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   is.c -o is.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bntseq.c -o bntseq.o
bntseq.c: In function ‘bns_restore_core’:
bntseq.c:98:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
   ^
bntseq.c:106:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp, "%u%s", &p->gi, str);
    ^
bntseq.c:114:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
    ^
bntseq.c:123:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
   ^
bntseq.c:129:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp, "%lld%d%s", &xx, &p->len, str);
    ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtmisc.c -o bwtmisc.o
bwtmisc.c: In function ‘bwa_pac_rev_core’:
bwtmisc.c:163:20: warning: variable ‘j’ set but not used [-Wunused-but-set-variable]
  bwtint_t pac_len, j;
                    ^
In file included from bwtmisc.c:35:0:
bwtmisc.c: At top level:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
bwtmisc.c: In function ‘bwa_seq_len’:
bwtmisc.c:51:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&c, 1, 1, fp);
  ^
bwtmisc.c: In function ‘bwt_pac2bwt’:
bwtmisc.c:72:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(buf2, 1, pac_size, fp);
  ^
bwtmisc.c: In function ‘bwa_pac_rev_core’:
bwtmisc.c:171:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(bufin, 1, pac_len, fp);
  ^
bwtmisc.c: In function ‘bwa_pac2cspac_core’:
bwtmisc.c:209:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtindex.c -o bwtindex.o
In file included from bwtindex.c:35:0:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   stdaln.c -o stdaln.o
stdaln.c: In function ‘aln_local_core’:
stdaln.c:545:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
  int gap_open, gap_ext, b;
                         ^
stdaln.c: In function ‘aln_extend_core’:
stdaln.c:865:16: warning: variable ‘tmp_len’ set but not used [-Wunused-but-set-variable]
  int q, r, qr, tmp_len;
                ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   simple_dp.c -o simple_dp.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwaseqio.c -o bwaseqio.o
In file included from bwtaln.h:5:0,
                 from bwaseqio.c:3:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwase.c -o bwase.o
bwase.c: In function ‘bwa_aln2seq_core’:
bwase.c:75:15: warning: variable ‘k’ set but not used [-Wunused-but-set-variable]
     int j, i, k;
               ^
bwase.c: In function ‘bwa_print_sam1’:
bwase.c:452:17: warning: variable ‘m_is_N’ set but not used [-Wunused-but-set-variable]
    int m_seqid, m_is_N;
                 ^
In file included from bwase.h:5:0,
                 from bwase.c:8:
bwase.c: At top level:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
bwase.c: In function ‘bwa_refine_gapped’:
bwase.c:315:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(ntpac, 1, ntbns->l_pac/4 + 1, ntbns->fp_pac);
   ^
bwase.c:321:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
   ^
bwase.c: In function ‘bwa_sai2sam_se_core’:
bwase.c:608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
  ^
bwase.c:624:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&n_aln, 4, 1, fp_sa);
    ^
bwase.c:629:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
    ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwape.c -o bwape.o
In file included from bwtaln.h:5:0,
                 from bwape.c:7:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
bwape.c: In function ‘bwa_cal_pac_pos_pe’:
bwape.c:308:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&n_aln, 4, 1, fp_sa[j]);
    ^
bwape.c:312:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]);
    ^
bwape.c: In function ‘bwa_paired_sw’:
bwape.c:517:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
   ^
bwape.c: In function ‘bwa_sai2sam_pe_core’:
bwape.c:673:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
  ^
bwape.c:676:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
  ^
bwape.c:689:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
    ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   kstring.c -o kstring.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   cs2nt.c -o cs2nt.o
In file included from bwtaln.h:5:0,
                 from cs2nt.c:4:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtsw2_core.c -o bwtsw2_core.o
In file included from bwtsw2.h:7:0,
                 from bwtsw2_core.c:7:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
In file included from bwtsw2_core.c:6:0:
bwt_lite.h:22:14: warning: inline function ‘bwtl_2occ4’ declared but never defined
  inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
              ^
bwt_lite.h:21:14: warning: inline function ‘bwtl_occ4’ declared but never defined
  inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
              ^
bwt_lite.h:20:18: warning: inline function ‘bwtl_occ’ declared but never defined
  inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtsw2_main.c -o bwtsw2_main.o
In file included from bwtsw2.h:6:0,
                 from bwtsw2_main.c:7:
bwt_lite.h:22:14: warning: inline function ‘bwtl_2occ4’ declared but never defined
  inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
              ^
bwt_lite.h:21:14: warning: inline function ‘bwtl_occ4’ declared but never defined
  inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
              ^
bwt_lite.h:20:18: warning: inline function ‘bwtl_occ’ declared but never defined
  inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
                  ^
In file included from bwtsw2_main.c:6:0:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtsw2_aux.c -o bwtsw2_aux.o
bwtsw2_aux.c: In function ‘gen_cigar’:
bwtsw2_aux.c:193:7: warning: variable ‘score’ set but not used [-Wunused-but-set-variable]
   int score, path_len, beg, end;
       ^
In file included from bwtsw2.h:7:0,
                 from bwtsw2_aux.c:13:
bwtsw2_aux.c: At top level:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
In file included from bwtsw2_aux.c:11:0:
bwt_lite.h:22:14: warning: inline function ‘bwtl_2occ4’ declared but never defined
  inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
              ^
bwt_lite.h:21:14: warning: inline function ‘bwtl_occ4’ declared but never defined
  inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
              ^
bwt_lite.h:20:18: warning: inline function ‘bwtl_occ’ declared but never defined
  inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
                  ^
bwtsw2_aux.c: In function ‘bsw2_aln’:
bwtsw2_aux.c:608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtsw2_chain.c -o bwtsw2_chain.o
In file included from bwtsw2.h:7:0,
                 from bwtsw2_chain.c:2:
bwt.h:96:14: warning: inline function ‘bwt_2occ4’ declared but never defined
  inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
              ^
bwt.h:95:14: warning: inline function ‘bwt_2occ’ declared but never defined
  inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
              ^
bwt.h:90:14: warning: inline function ‘bwt_occ4’ declared but never defined
  inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
              ^
bwt.h:89:18: warning: inline function ‘bwt_occ’ declared but never defined
  inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
                  ^
In file included from bwtsw2.h:6:0,
                 from bwtsw2_chain.c:2:
bwt_lite.h:22:14: warning: inline function ‘bwtl_2occ4’ declared but never defined
  inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
              ^
bwt_lite.h:21:14: warning: inline function ‘bwtl_occ4’ declared but never defined
  inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
              ^
bwt_lite.h:20:18: warning: inline function ‘bwtl_occ’ declared but never defined
  inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
                  ^
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bamlite.c -o bamlite.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   main.c -o main.o
gcc -g -Wall -O2 -DHAVE_PTHREAD  utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
bwtaln.o: In Funktion `bwt_cal_width':
/home/pogopanther/Downloads/bwa-0.5.10/bwtaln.c:61: Nicht definierter Verweis auf `bwt_2occ'
bwtgap.o: In Funktion `bwt_match_gap':
/home/pogopanther/Downloads/bwa-0.5.10/bwtgap.c:201: Nicht definierter Verweis auf `bwt_2occ4'
bwtsw2_core.o: In Funktion `bsw2_connectivity':
/home/pogopanther/Downloads/bwa-0.5.10/bwtsw2_core.c:104: Nicht definierter Verweis auf `bwtl_2occ4'
bwtsw2_core.o: In Funktion `bsw2_core':
/home/pogopanther/Downloads/bwa-0.5.10/bwtsw2_core.c:476: Nicht definierter Verweis auf `bwtl_2occ4'
/home/pogopanther/Downloads/bwa-0.5.10/bwtsw2_core.c:529: Nicht definierter Verweis auf `bwt_2occ4'
collect2: error: ld returned 1 exit status
Makefile:38: die Regel für Ziel „bwa“ scheiterte
make: *** [bwa] Fehler 1

Sorry for german messeages. In general the compiler complains that the functions wt_2occ4 and bwt_2occ are missing. I made the binaries on a different machine without any errors. This computer must be missing anything but from this error I cannot tell what. I think I will have to contact the bwa guys.

Mathias

[Márton Münz]

Hi Mathias,

 

In this other thread you wrote that you had overcome the bwa issue. Did it turn out to be unrelated to OpEx?

 

Thanks,

Márton

[nealc...@gmail.com]

Hi Márton,

I had the same problem, and it turns out to be an issue only with bwa, not with OpEx. However, later versions of bwa (I tried 0.7.12) seem to compile without issue on my 64-bit Linux machine.

My correction was just to copy and paste the functions into the files that were missing them.

Thanks,
Neal

[Márton Münz]

Hi Neal,

Great! Very useful to know. Thanks very much for sharing this information! 

Best wishes,

Márton