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I am trying to compile simNGS, but it fails. I get these messages found below. Obviously it is a linking problem.
Download simNGS from http://www.ebi.ac.uk/goldman-srv/simNGS/ or https://github.com/timmassingham/simNGS and both result in errors. The error messages came from compiling code from the second link. I am using Ubuntu 11.10.
Someone is probably going to recommend dwgsim. The thing is that I would like random reads whose phred-scaled base quality scores have some random variation. dwgsim generates clones. I am using dwgsim too, but I need an alternative for comparison.
Download simNGS from http://www.ebi.ac.uk/goldman-srv/simNGS/ or https://github.com/timmassingham/simNGS and both result in errors. The error messages came from compiling code from the second link. I am using Ubuntu 11.10.
Someone is probably going to recommend dwgsim. The thing is that I would like random reads whose phred-scaled base quality scores have some random variation. dwgsim generates clones. I am using dwgsim too, but I need an alternative for comparison.
Code:
dagge@dagge-Dell-System-XPS-L502X:~/lib/timmassingham-simNGS-54639a9/src$ make -B -f Makefile.linux gcc -o sfmt.o -msse2 -DHAVE_SSE2 -O9 -finline-functions -fomit-frame-pointer -DNDEBUG -fno-strict-aliasing --param max-inline-insns-single=1800 -std=c99 -DMEXP=19937 -ISFMT-src-1.3/ -c SFMT-src-1.3/SFMT.c gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o matrix.o -c matrix.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o nuc.o -c nuc.c gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o intensities.o -c intensities.c intensities.c: In function ‘new_MODEL_from_fp’: intensities.c:226:16: warning: ignoring return value of ‘getline’, declared with attribute warn_unused_result [-Wunused-result] intensities.c:243:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o normal.o -c normal.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o weibull.o -c weibull.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o sequence.o -c sequence.c gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o mystring.o -c mystring.c gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o simNGS.o -c simNGS.c gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o utility.o -c utility.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] utility.c: In function ‘read_real_t’: utility.c:138:47: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_double’: utility.c:131:47: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_float’: utility.c:124:44: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_uint64_t’: utility.c:116:54: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_uint32_t’: utility.c:108:54: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_uint16_t’: utility.c:100:54: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_uint8_t’: utility.c:93:51: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_int64_t’: utility.c:86:51: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_int32_t’: utility.c:79:51: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_int16_t’: utility.c:72:51: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_int8_t’: utility.c:65:48: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] utility.c: In function ‘read_int’: utility.c:58:38: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o random.o -c random.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o kumaraswamy.o -c kumaraswamy.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o elliptic.o -c elliptic.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] elliptic.c:35:15: warning: ‘lognormal_mean’ defined but not used [-Wunused-variable] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o lambda_distribution.o -c lambda_distribution.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] lambda_distribution.c: In function ‘new_Distribution_from_fp’: lambda_distribution.c:104:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] lambda_distribution.c:106:19: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o mixnormal.o -c mixnormal.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o normal_ziggurat.o -c normal_ziggurat.c utility.h:42:15: warning: ‘reallocf’ defined but not used [-Wunused-function] gcc -D_GNU_SOURCE -DUSE_BLAS -Wall -O3 -funroll-loops -DNDEBUG -fomit-frame-pointer -std=gnu99 -msse2 -o ../bin/simNGS -lm -lc -lblas -llapack sfmt.o matrix.o nuc.o intensities.o normal.o weibull.o sequence.o mystring.o simNGS.o utility.o random.o kumaraswamy.o elliptic.o lambda_distribution.o mixnormal.o normal_ziggurat.o simNGS.o: In function `parse_arguments': simNGS.c:(.text+0x2664): undefined reference to `sqrt' simNGS.o: In function `correlated_distribution': simNGS.c:(.text+0x43a8): undefined reference to `sqrt' simNGS.o: In function `main': simNGS.c:(.text.startup+0x2e79): undefined reference to `log10' simNGS.c:(.text.startup+0x2ef4): undefined reference to `log10' simNGS.c:(.text.startup+0x2f13): undefined reference to `log10' simNGS.c:(.text.startup+0x3022): undefined reference to `log10' simNGS.c:(.text.startup+0x3090): undefined reference to `log10' simNGS.o:simNGS.c:(.text.startup+0x30b1): more undefined references to `log10' follow simNGS.o: In function `main': simNGS.c:(.text.startup+0x3896): undefined reference to `sqrt' simNGS.c:(.text.startup+0x38d4): undefined reference to `sqrt' simNGS.c:(.text.startup+0x392a): undefined reference to `sqrt' simNGS.c:(.text.startup+0x3968): undefined reference to `sqrt' matrix.o: In function `cholesky': matrix.c:(.text+0x112a): undefined reference to `dpotrf_' matrix.o: In function `invert_cholesky': matrix.c:(.text+0x134f): undefined reference to `dtrtri_' matrix.o: In function `invert_MAT': matrix.c:(.text+0x2772): undefined reference to `dgetri_' matrix.c:(.text+0x2819): undefined reference to `dgetrf_' matrix.c:(.text+0x2839): undefined reference to `dgetri_' nuc.o: In function `phredchar_from_prob': nuc.c:(.text+0x139f): undefined reference to `log1p' intensities.o: In function `trim_MODEL': intensities.c:(.text+0x1fed): undefined reference to `sqrt' intensities.o: In function `likelihood_cycle_intensities': intensities.c:(.text+0x2d2d): undefined reference to `log' intensities.c:(.text+0x2d6a): undefined reference to `log' intensities.c:(.text+0x302d): undefined reference to `log' intensities.c:(.text+0x307e): undefined reference to `exp' intensities.c:(.text+0x3083): undefined reference to `log1p' intensities.c:(.text+0x30d2): undefined reference to `exp' intensities.c:(.text+0x30d7): undefined reference to `log1p' intensities.c:(.text+0x3111): undefined reference to `exp' intensities.c:(.text+0x3116): undefined reference to `log1p' intensities.c:(.text+0x3149): undefined reference to `exp' intensities.c:(.text+0x314e): undefined reference to `log1p' intensities.c:(.text+0x318b): undefined reference to `exp' intensities.c:(.text+0x3190): undefined reference to `log1p' intensities.c:(.text+0x31c2): undefined reference to `exp' intensities.c:(.text+0x31c7): undefined reference to `log1p' intensities.c:(.text+0x31fb): undefined reference to `exp' intensities.c:(.text+0x3200): undefined reference to `log1p' intensities.c:(.text+0x322c): undefined reference to `exp' intensities.c:(.text+0x3231): undefined reference to `log1p' intensities.o: In function `fuzz_prob': intensities.c:(.text+0x3b31): undefined reference to `atanh' intensities.c:(.text+0x3b9e): undefined reference to `tanh' intensities.o: In function `quality_from_likelihood': intensities.c:(.text+0x3ca3): undefined reference to `exp' intensities.c:(.text+0x3cd2): undefined reference to `exp' intensities.c:(.text+0x3cfb): undefined reference to `exp' intensities.c:(.text+0x3d24): undefined reference to `exp' intensities.o: In function `dchisq4': intensities.c:(.text+0x2991): undefined reference to `exp' normal.o: In function `pstdnorm': normal.c:(.text+0xb1): undefined reference to `erf' normal.c:(.text+0xe1): undefined reference to `erfc' normal.o: In function `qstdnorm': normal.c:(.text+0x10d): undefined reference to `log' normal.c:(.text+0x143): undefined reference to `log1p' normal.c:(.text+0x171): undefined reference to `erf' normal.c:(.text+0x1a9): undefined reference to `exp' normal.c:(.text+0x2b1): undefined reference to `erfc' normal.c:(.text+0x2e9): undefined reference to `exp' normal.o: In function `dnorm': normal.c:(.text+0x383): undefined reference to `log' normal.c:(.text+0x3aa): undefined reference to `exp' normal.o: In function `pnorm': normal.c:(.text+0x3d9): undefined reference to `erf' normal.c:(.text+0x401): undefined reference to `erfc' normal.o: In function `rmultinorm': normal.c:(.text+0x6b5): undefined reference to `dtrmv_' normal.o: In function `dmultinorm': normal.c:(.text+0xe8a): undefined reference to `exp' normal.c:(.text+0xeb6): undefined reference to `pow' normal.c:(.text+0x12ba): undefined reference to `log' normal.c:(.text+0x1402): undefined reference to `sqrt' normal.o: In function `dstdnorm': normal.c:(.text+0x91): undefined reference to `exp' normal.o: In function `pstdnorm': normal.c:(.text+0xd2): undefined reference to `log' normal.o: In function `pnorm': normal.c:(.text+0x3fa): undefined reference to `log' normal.o: In function `rlognorm': normal.c:(.text+0x492): undefined reference to `exp' weibull.o: In function `pweibull': weibull.c:(.text+0xa3): undefined reference to `pow' weibull.c:(.text+0xdc): undefined reference to `exp' weibull.c:(.text+0xf9): undefined reference to `expm1' weibull.o: In function `qweibull': weibull.c:(.text+0x1a0): undefined reference to `log1p' weibull.c:(.text+0x1e1): undefined reference to `log' weibull.c:(.text+0x1f6): undefined reference to `log' weibull.c:(.text+0x233): undefined reference to `log' weibull.c:(.text+0x27b): undefined reference to `pow' weibull.o: In function `dweibull': weibull.c:(.text+0x2eb): undefined reference to `pow' weibull.c:(.text+0x315): undefined reference to `exp' weibull.c:(.text+0x35c): undefined reference to `log' weibull.c:(.text+0x371): undefined reference to `log' weibull.c:(.text+0x38f): undefined reference to `pow' weibull.o: In function `rweibull': weibull.c:(.text+0x47f): undefined reference to `log' weibull.c:(.text+0x4a0): undefined reference to `pow' weibull.o: In function `pweibull': weibull.c:(.text+0xcc): undefined reference to `exp' weibull.c:(.text+0xef): undefined reference to `log1p' random.o: In function `rgamma1': random.c:(.text+0x2f5): undefined reference to `tan' random.c:(.text+0x343): undefined reference to `log' random.c:(.text+0x358): undefined reference to `exp' random.c:(.text+0x3a3): undefined reference to `sqrt' random.o: In function `rgamma2': random.c:(.text+0x3d6): undefined reference to `exp' random.c:(.text+0x3fe): undefined reference to `exp2' random.c:(.text+0x42c): undefined reference to `expm1' random.c:(.text+0x43f): undefined reference to `pow' random.c:(.text+0x472): undefined reference to `pow' random.c:(.text+0x490): undefined reference to `exp' random.c:(.text+0x503): undefined reference to `pow' random.c:(.text+0x518): undefined reference to `log1p' random.c:(.text+0x56f): undefined reference to `pow' random.c:(.text+0x5a3): undefined reference to `exp' random.c:(.text+0x5b4): undefined reference to `exp2' random.c:(.text+0x5cb): undefined reference to `expm1' random.c:(.text+0x5de): undefined reference to `pow' random.c:(.text+0x63e): undefined reference to `pow' random.c:(.text+0x680): undefined reference to `log' random.o: In function `rexp': random.c:(.text+0x6c7): undefined reference to `log' random.o: In function `rgamma': random.c:(.text+0x757): undefined reference to `log' random.o: In function `rchisq': random.c:(.text+0x7f5): undefined reference to `log' kumaraswamy.o: In function `pkumaraswamy': kumaraswamy.c:(.text+0xa6): undefined reference to `log' kumaraswamy.c:(.text+0xb5): undefined reference to `expm1' kumaraswamy.c:(.text+0xc2): undefined reference to `log' kumaraswamy.c:(.text+0xf1): undefined reference to `expm1' kumaraswamy.o: In function `qkumaraswamy': kumaraswamy.c:(.text+0x13c): undefined reference to `exp' kumaraswamy.c:(.text+0x167): undefined reference to `log1p' kumaraswamy.c:(.text+0x1b5): undefined reference to `expm1' kumaraswamy.c:(.text+0x1cf): undefined reference to `log' kumaraswamy.c:(.text+0x1e0): undefined reference to `exp' kumaraswamy.c:(.text+0x224): undefined reference to `pow' kumaraswamy.c:(.text+0x25e): undefined reference to `log1p' kumaraswamy.c:(.text+0x287): undefined reference to `exp' kumaraswamy.o: In function `dkumaraswamy': kumaraswamy.c:(.text+0x2e4): undefined reference to `log' kumaraswamy.c:(.text+0x2f5): undefined reference to `expm1' kumaraswamy.c:(.text+0x310): undefined reference to `log' kumaraswamy.c:(.text+0x325): undefined reference to `log' kumaraswamy.c:(.text+0x336): undefined reference to `log' kumaraswamy.c:(.text+0x353): undefined reference to `log' kumaraswamy.o: In function `rkumaraswamy': kumaraswamy.c:(.text+0x443): undefined reference to `pow' kumaraswamy.c:(.text+0x454): undefined reference to `log1p' kumaraswamy.o: In function `pkumaraswamy': kumaraswamy.c:(.text+0xe4): undefined reference to `exp' kumaraswamy.c:(.text+0x107): undefined reference to `log' kumaraswamy.o: In function `qkumaraswamy': kumaraswamy.c:(.text+0x187): undefined reference to `exp' kumaraswamy.o: In function `dkumaraswamy': kumaraswamy.c:(.text+0x3a8): undefined reference to `exp' kumaraswamy.o: In function `rkumaraswamy': kumaraswamy.c:(.text+0x474): undefined reference to `exp' elliptic.o: In function `normal_radius': elliptic.c:(.text+0x81): undefined reference to `sqrt' elliptic.o: In function `lognormal_radius': elliptic.c:(.text+0x99): undefined reference to `log' elliptic.c:(.text+0xc6): undefined reference to `sqrt' elliptic.o: In function `relliptic_cycle': elliptic.c:(.text+0x8e1): undefined reference to `sqrt' elliptic.o: In function `relliptic': elliptic.c:(.text+0x107a): undefined reference to `dtrmv_' elliptic.c:(.text+0x198d): undefined reference to `sqrt' lambda_distribution.o: In function `qdistribution': lambda_distribution.c:(.text+0x10b2): undefined reference to `atanh' lambda_distribution.c:(.text+0x116b): undefined reference to `expm1' lambda_distribution.o: In function `qlogistic': lambda_distribution.c:(.text+0x11b4): undefined reference to `atanh' lambda_distribution.c:(.text+0x11e6): undefined reference to `expm1' mixnormal.o: In function `initialise_mixture': mixnormal.c:(.text+0xc04): undefined reference to `sqrt' mixnormal.o: In function `emstep_mixnormal': mixnormal.c:(.text+0xd1a): undefined reference to `log' mixnormal.c:(.text+0xd34): undefined reference to `log' mixnormal.c:(.text+0xd91): undefined reference to `log' mixnormal.c:(.text+0xdb1): undefined reference to `log' mixnormal.c:(.text+0xde5): undefined reference to `log' mixnormal.o:mixnormal.c:(.text+0xe01): more undefined references to `log' follow mixnormal.o: In function `emstep_mixnormal': mixnormal.c:(.text+0x12df): undefined reference to `exp' mixnormal.c:(.text+0x134d): undefined reference to `exp' mixnormal.c:(.text+0x1381): undefined reference to `exp' mixnormal.c:(.text+0x13bb): undefined reference to `exp' mixnormal.c:(.text+0x13f5): undefined reference to `exp' mixnormal.o:mixnormal.c:(.text+0x142f): more undefined references to `exp' follow mixnormal.o: In function `emstep_mixnormal': mixnormal.c:(.text+0x1637): undefined reference to `log' mixnormal.c:(.text+0x232d): undefined reference to `log' mixnormal.c:(.text+0x2385): undefined reference to `sqrt' mixnormal.c:(.text+0x23d1): undefined reference to `sqrt' mixnormal.c:(.text+0x2420): undefined reference to `sqrt' mixnormal.c:(.text+0x2476): undefined reference to `sqrt' mixnormal.o: In function `qmixnorm': mixnormal.c:(.text+0x2c52): undefined reference to `log' mixnormal.c:(.text+0x2c69): undefined reference to `log1p' mixnormal.c:(.text+0x3044): undefined reference to `exp' mixnormal.c:(.text+0x305e): undefined reference to `expm1' mixnormal.c:(.text+0x30c5): undefined reference to `sqrt' mixnormal.o: In function `dmixnorm': mixnormal.c:(.text+0x2787): undefined reference to `log' mixnormal.o: In function `pmixnorm': mixnormal.c:(.text+0x28ec): undefined reference to `log' normal_ziggurat.o: In function `rstdnorm_zig': normal_ziggurat.c:(.text+0xd1): undefined reference to `exp' normal_ziggurat.c:(.text+0x1c0): undefined reference to `log' normal_ziggurat.c:(.text+0x220): undefined reference to `log' collect2: ld returned 1 exit status make: *** [simNGS] Error 1
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