[GenoMax]

Likely missing parts highlighted in red. Try the command below:

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | [COLOR="Red"]/[/COLOR]User/user/tan_analysis/samtools-0.1.19/bcftools[COLOR="Red"]/bcftools[/COLOR] view -bvcg - > eg2.raw.bcf

[maivantan]

It was stil not working

SER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | /User/user/tan_analysis/samtools-0.1.19/bcftools/bcftools view -bvcg - > eg2.raw.bcf
-bash: /User/user/tan_analysis/samtools-0.1.19/bcftools/bcftools: No such file or directory
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

[GenoMax]

Can you verify that the "bcftools" executable is present (based on the error you are getting it appears to have not been "made" when you compiled samtools).

Post the listing of this directory:

$ ls -l /User/user/tan_analysis/samtools-0.1.19/bcftools/

[maivantan]

Here the results

total 2096
-rw-r-----@ 1 user staff 1232 3 19 2013 Makefile
-rw-r----- 1 user staff 1966 3 19 2013 README
-rw-r-----@ 1 user staff 10569 3 19 2013 bcf.c
-rw-r-----@ 1 user staff 7223 3 19 2013 bcf.h
-rw-r-----@ 1 user staff 7226 3 19 2013 bcf.h~
-rw-r--r-- 1 user staff 40332 10 28 20:57 bcf.o
-rw-r-----@ 1 user staff 4217 3 19 2013 bcf.tex
-rw-r-----@ 1 user staff 3028 3 19 2013 bcf2qcall.c
-rw-r--r-- 1 user staff 7468 10 28 20:57 bcf2qcall.o
-rwxr-xr-x 1 user staff 166644 10 28 20:57 bcftools
-rw-r-----@ 1 user staff 13251 3 19 2013 bcfutils.c
-rw-r--r-- 1 user staff 42172 10 28 20:57 bcfutils.o
-rw-r-----@ 1 user staff 26288 3 19 2013 call1.c
-rw-r--r-- 1 user staff 60648 10 28 20:57 call1.o
-rw-r-----@ 1 user staff 8985 3 19 2013 em.c
-rw-r--r-- 1 user staff 21156 10 28 20:57 em.o
-rw-r-----@ 1 user staff 3122 3 19 2013 fet.c
-rw-r--r-- 1 user staff 8120 10 28 20:57 fet.o
-rw-r-----@ 1 user staff 8256 3 19 2013 index.c
-rw-r--r-- 1 user staff 25444 10 28 20:57 index.o
-rw-r-----@ 1 user staff 4960 3 19 2013 kfunc.c
-rw-r--r-- 1 user staff 18228 10 28 20:57 kfunc.o
-rw-r-----@ 1 user staff 7269 3 19 2013 kmin.c
-rw-r-----@ 1 user staff 1619 3 19 2013 kmin.h
-rw-r--r-- 1 user staff 11968 10 28 20:57 kmin.o
-rw-r--r-- 1 user staff 293456 10 28 20:57 libbcf.a
-rw-r-----@ 1 user staff 5184 3 19 2013 main.c
-rw-r--r-- 1 user staff 17652 10 28 20:57 main.o
-rw-r-----@ 1 user staff 3816 3 19 2013 mut.c
-rw-r--r-- 1 user staff 11060 10 28 20:57 mut.o
-rw-r-----@ 1 user staff 33429 3 19 2013 prob1.c
-rw-r-----@ 1 user staff 1457 3 19 2013 prob1.h
-rw-r--r-- 1 user staff 77440 10 28 20:57 prob1.o
-rw-r-----@ 1 user staff 7040 3 19 2013 vcf.c
-rw-r--r-- 1 user staff 27272 10 28 20:57 vcf.o
-rwxr-x---@ 1 user staff 15707 3 19 2013 vcfutils.pl

[GenoMax]

As you can see the "bcftools" binary file is present in the /User/user/tan_analysis/samtools-0.1.19/bcftools/ directory. It also has execute permissions that are needed to "run" a program.

[maivantan]

Dear GenoMax
I tried bellow commands, i think it worked.

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | ~/tan_analysis/samtools-0.1.19/bcftools/bcftools view -bvcg - > eg2.raw.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[afs] 0:4254.406 1:3.562 2:113.032
USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ ~/tan_analysis/samtools-0.1.19/bcftools/bcftools view eg2.raw.bcf
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT eg2.sorted.bam
gi|9626243|ref|NC_001416.1| 2 . GGCG GGCGCGGGGGCG 5.08 . INDEL;IS=1,0.500000;DP=2;AF1=1;AC1=2;DP4=0,0,1,0;MQ=42;FQ=-37.5 GT:PL:GQ 1/1:41,3,0:3
gi|9626243|ref|NC_001416.1| 244 . CA C 30.6 . INDEL;IS=1,0.028571;DP=35;VDB=1.039505e-01;AF1=1;AC1=2;DP4=0,0,4,2;MQ=37;FQ=-52.5 GT:PL:GQ 1/1:71,18,0:33
gi|9626243|ref|NC_001416.1| 245 . ATT AT 194 . INDEL;IS=33,0.942857;DP=34;VDB=2.115336e-01;AF1=1;AC1=2;DP4=0,0,13,12;MQ=37;FQ=-110 GT:PL:GQ 1/1:235,75,0:99
gi|

is it correct? can you check it?

Thank you very much

[GenoMax]

It does look like the command worked this time. You should be set to go to the next step.

[maivantan]

yes,
I am looking how go to next steps.
Do you have any suggestion?
Thank you very much again

[GenoMax]

I though you were following the guide on multisample SNP calling on this page: http://samtools.sourceforge.net/mpileup.shtml

[maivantan]

i am going to try it.
Thank you very much GenoMax,

[Hamid]

installing samtools on mac

Hi,

Does anyone have a guide on how to properly install samtools version 0.1.19 on a macbook pro with osx 10.9.2.
I would greatly appreciate your help.

Thank you.

Hamid

[GenoMax]

Hi,

Does anyone have a guide on how to properly install samtools version 0.1.19 on a macbook pro with osx 10.9.2.
I would greatly appreciate your help.

Thank you.

Hamid

1. Download and install Xcode 5.1 from app store if you have not done so already.
2. Download samtools source from: http://sourceforge.net/projects/samt...d?source=files
3. Change to the directory where you downloaded the source file.

$ bunzip2 samtools*.bz2
$ tar -xvf samtools-0.1.19.tar
$ cd samtools-0.1.19
$ make

If all goes well there should be an executable produced that you can test run

$ ./samtools

You strictly do not have to "install", but if you want you could copy the executable to a directory that is in your $PATH in case you do not want to provide full path to the samtools executable when you run it.

[Hamid]

Thank you very much GenoMax...It worked great.

Is it possible to have the commands be universally available from any directory without having to specify the path?

Thank you

hamid

[GenoMax]

You can copy the samtools executable to a directory in your $PATH.

$ echo $PATH

Following assumes that you have a /usr/local/bin and it is in your $PATH. If this directory does not exist then you could choose to use /bin.

Go to the directory containing the samtools executable and do the following:

$ sudo cp samtools /usr/local/bin

That should allow you to run samtools (or other executables) without having to provide full path each time.

[beline]

Error installing samtools to my Mac

1. Download and install Xcode 5.1 from app store if you have not done so already.
2. Download samtools source from: http://sourceforge.net/projects/samt...d?source=files
3. Change to the directory where you downloaded the source file.

$ bunzip2 samtools*.bz2
$ tar -xvf samtools-0.1.19.tar
$ cd samtools-0.1.19
$ make

If all goes well there should be an executable produced that you can test run

$ ./samtools

You strictly do not have to "install", but if you want you could copy the executable to a directory that is in your $PATH in case you do not want to provide full path to the samtools executable when you run it.

I am having trouble with this exact scenario. After I typing the command "make" I get this error message:

gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:228:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:197:1: note: expanded from here
kh_clear_s
^
bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:211:1: note: expanded from here
kh_del_s
^
bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
KHASH_MAP_INIT_STR(r2l, str_p)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
SCOPE kh_##name##_t *kh_init_##name() { \
^
<scratch space>:218:1: note: expanded from here
kh_init_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_destroy_##name(kh_##name##_t *h) \
^
<scratch space>:223:1: note: expanded from here
kh_destroy_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:226:1: note: expanded from here
kh_clear_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:229:1: note: expanded from here
kh_get_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
^
<scratch space>:235:1: note: expanded from here
kh_put_r2l
^
bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:240:1: note: expanded from here
kh_del_r2l
^
8 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
KHASH_MAP_INIT_STR(ref, uint64_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:197:1: note: expanded from here
kh_clear_ref
^
bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
^
<scratch space>:200:1: note: expanded from here
kh_get_ref
^
bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:211:1: note: expanded from here
kh_del_ref
^
3 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:211:1: note: expanded from here
kh_clear_i
^
bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:225:1: note: expanded from here
kh_del_i
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:154:1: note: expanded from here
kh_clear_s
^
faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:168:1: note: expanded from here
kh_del_s
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:207:1: note: expanded from here
kh_clear_reg
^
bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:221:1: note: expanded from here
kh_del_reg
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, const char *)
^
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:154:1: note: expanded from here
kh_clear_str
^
sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:168:1: note: expanded from here
kh_del_str
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
vcf.c:238:15: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
endblock: i = i;
~ ^ ~
vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 4096)
^
../kseq.h:142:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:66:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
bcfutils.c:6:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
KHASH_MAP_INIT_STR(str2id, int)
^
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:37:1: note: expanded from here
kh_clear_str2id
^
bcfutils.c:6:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:51:1: note: expanded from here
kh_del_str2id
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
prob1.c:10:1: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT(gzFile, gzread, 16384)
^
../kseq.h:142:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETC(__read, __bufsize) \
^
../kseq.h:66:20: note: expanded from macro '__KS_GETC'
static inline int ks_getc(kstream_t *ks) \
^
1 warning generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
/bin/sh: line 0: cd: misc: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
make[1]: *** [lib-recur] Error 1
make: *** [all-recur] Error 1

When I attempt the "make" command again I get the abbreviated version:

make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
/bin/sh: line 0: cd: misc: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Tiger: No such file or directory
make[1]: *** [lib-recur] Error 1
make: *** [all-recur] Error 1

I've tried this with both samtools 0.1.18 and 0.1.19. Any thoughts?