problem installing Pindel

[godzilla07]

I have been trying to install pindel 0.2.4t on my Mac OS X 7.5 and I get an error message.

bash-3.2$ less INSTALL
bash-3.2$ ./INSTALL /Users/davidkowbel/samtools-0.1.19/
path is now: /Users/davidkowbel/samtools-0.1.19/
make -C src pindel
parameter.cpp:26:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
pindel.cpp:28:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
parameter.cpp:26:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
pindel.cpp:28:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
c++ -Wall -g -c -O3 -fopenmp -I/Users/davidkowbel/samtools-0.1.19/ pindel.cpp -o pindel.o
clang: warning: argument unused during compilation: '-fopenmp'
pindel.cpp:28:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
make[1]: *** [pindel.o] Error 1
make: *** [pindel] Error 2

Creating pindel2vcf utility...
pindel2vcf created.

Creating sam2pindel utility...
sam2pindel created.
mv: rename src/pindel to ./pindel: No such file or directory

Pindel successfully compiled. The pindel executable can be found in this directory.
I have installed Xcode 4.6 . I don't know why the header file omp.h cannot be found?

[KaiYe]

your compiler does not have library set up correctly.

try gcc compiler

https://github.com/kennethreitz/osx-gcc-installer/downloads

I had the same issue when I upgraded my xcode. installing gcc compiler solves this.

[KaiYe]

update from the experts in my institute

"Yep. I'd probably use that, someone on biostars suggests using the homebrew version. The issue is indeed that LLVM/clang does not currently support OpenMP and so you need to fall back to GCC"

"GCC is now maintained in homebrew-versions, with major version
number in formula name as suffix. Please tap using:
$ brew search gcc
brew tap homebrew/versions

and then install GCC based on its version, e.g., 'brew install gcc47'."

[tonio100680]

After use samtools sam2pindel then I execute Pindel. Here is what I get ....

$ pindel -f [PATH]/human_g1k_v37.fasta -p [PATH]/pindel/input_pindel.txt -c 17:41,194,312-41,279,500 -o [PATH]/pindel/EI17_Pindel
Pindel version 0.2.4t, August 13 2012.
Processing chromosome: 1
Skipping chromosome: 1
Processing chromosome: 2
Skipping chromosome: 2
Processing chromosome: 3
Skipping chromosome: 3
Processing chromosome: 4
Skipping chromosome: 4
Processing chromosome: 5
Skipping chromosome: 5
Processing chromosome: 6
Skipping chromosome: 6
Processing chromosome: 7
Skipping chromosome: 7
Processing chromosome: 8
Skipping chromosome: 8
Processing chromosome: 9
Skipping chromosome: 9
Processing chromosome: 10
Skipping chromosome: 10
Processing chromosome: 11
Skipping chromosome: 11
Processing chromosome: 12
Skipping chromosome: 12
Processing chromosome: 13
Skipping chromosome: 13
Processing chromosome: 14
Skipping chromosome: 14
Processing chromosome: 15
Skipping chromosome: 15
Processing chromosome: 16
Skipping chromosome: 16
Processing chromosome: 17
Chromosome Size: 81195210
NumBoxes: 60004 BoxSize: 3373

Looking at chromosome 17 bases 41194312 to 41279500.
getReads 17 101195210
Scanning and processing reads anchored in 17
last one: 0 and UPCLOSE= 0

The last read Pindel scanned:
@PC-LABO-NGS-MIS_25:1:1103:23265:10796
TAAGGGTGGGTAGGTTTGTTGGTATCCTAGTGGGTGAGGGGTGGCTTTGGAGTTGCAGTTGATGTGTGATAGTTGAGGGTTGATTGCTGTACTTGCTTGTAAGCATGGGGGGGGGGGGTTTTGATGGGGTTTGGGTTTTTATGT
+ chrM 16129 254 220 patient

Number of reads in current window: 0, + 0 - 0
Number of reads where the close end could be mapped: 0, + 0 - 0
Percentage of reads which could be mapped: + 0.00% - 0.00%

No reads found in [PATH]/input_pindelbis.txt
There are no reads for this bin.
Loading genome sequences and reads: 0 seconds.
Mining, Sorting and output results: 0 seconds.

Do you have any idea?

Thank you in advance for your help

[KaiYe]

your reference genome has no "chr" while I saw chrM in your file. please notice that chr1 != 1

[godzilla07]

your compiler does not have library set up correctly.

try gcc compiler

https://github.com/kennethreitz/osx-gcc-installer/downloads

I had the same issue when I upgraded my xcode. installing gcc compiler solves this.

Thanks. That did the job!

[Jeromek]

Did you guys modify the makefile in any way? i did a brew install of gcc48, and have now modified the makefile in src with $(CXX)=g++-4.8 but still the same error

[wyll]

Hi,

I'm trying to run the demo files in pindel
/home/nina/linux/tools/pindel-m/pindel -f simulated_reference.fa -i simulated_config.txt -o output

but it gave me error message:
/home/nina/linux/tools/pindel-m/pindel: error while loading shared libraries: libhts.so.1: cannot open shared object file: No such file or directory

Is there a way to install the missing library?

I've tried
sudo make install libhts.so.1

It shows
mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig
install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.2.1
ln -sf libhts.so.1.2.1 /usr/local/lib/libhts.so
ln -sf libhts.so.1.2.1 /usr/local/lib/libhts.so.1
sed -e 's#@includedir@#/usr/local/include#g;s#@libdir@#/usr/local/lib#g;s#@PACKAGE_VERSION@#1.2.1#g' htslib.pc.in > /usr/local/lib/pkgconfig/htslib.pc
chmod 644 /usr/local/lib/pkgconfig/htslib.pc
install -p bgzip htsfile tabix /usr/local/bin
install -p -m 644 htslib/*.h /usr/local/include/htslib
install -p -m 644 libhts.a /usr/local/lib/libhts.a
install -p -m 644 htsfile.1 tabix.1 /usr/local/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5
make: Nothing to be done for `libhts.so.1'.

Thx!!

[GenoMax]

@wyll: See the last line here https://github.com/genome/pindel/blo...README_INSTALL

[wyll]

I've actually read that line over and over again for some time, but still wasn't able to understand it. Now that I go back and read again, I think I know how to type the command now. You have to add the rest of the command after ./pindel silly me...
@GenoMax: Thanks a bunch =D