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