Problem building Platypus and not finding variant caller

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wri...@nmsu.edu

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Jun 25, 2018, 5:41:26 PM6/25/18

to Platypus Users

Hi All,

I'm new to this group and Platypus but believe I am encountering an error similar to what others have found. Perhaps there is a common solution. I'm trying to use Platypus as part of the FastGBS script to extract SNP's from next gen sequencing of a hummingbird population. FastGBS throws an error

Traceback (most recent call last):

File "Platypus.py", line 9, in <module>

import runner

File "/Programs/Platypus_0.8.1/runner.py", line 9, in <module>

import variantcaller

ImportError: No module named variantcaller

When I look in the Platypus folder I indeed find a module named runner but none named variantcaller

wright@bailey-data:/Programs/Platypus_0.8.1$ ll

total 8768

drwxr-xr-x 5 501 staff 4096 May 2 22:01 ./

drwxr-xr-x 10 root root 4096 May 2 22:30 ../

-rwxr-xr-x 1 501 staff 214 Apr 7 2015 ._align.c*

-rwxr-xr-x 1 501 staff 14315 Apr 7 2015 align.c*

-rwxr-xr-x 1 501 staff 206 Apr 7 2015 ._align.h*

-rwxr-xr-x 1 501 staff 826 Apr 7 2015 align.h*

-rw-r--r-- 1 501 staff 486488 Apr 7 2015 assembler.c

drwxr-xr-x 4 root root 4096 May 2 22:01 build/

-rwxr-xr-x 1 501 staff 298 Apr 7 2015 ._buildPlatypus.sh*

-rwxr-xr-x 1 501 staff 417 Apr 7 2015 buildPlatypus.sh*

-rw-r--r-- 1 501 staff 210 Apr 7 2015 ._calign.c

-rw-r--r-- 1 501 staff 134601 Apr 7 2015 calign.c

-rw-r--r-- 1 501 staff 424071 Apr 7 2015 cerrormodel.c

-rw-r--r-- 1 501 staff 204562 Apr 7 2015 cgenotype.c

-rw-r--r-- 1 501 staff 476349 Apr 7 2015 chaplotype.c

-rw-r--r-- 1 501 staff 618198 Apr 7 2015 cpopulation.c

-rwxr-xr-x 1 501 staff 407232 Apr 7 2015 ctabix.c*

-rw-r--r-- 1 501 staff 378181 Apr 7 2015 cwindow.c

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._extendedoptparse.py*

-rwxr-xr-x 1 501 staff 2867 Apr 7 2015 extendedoptparse.py*

-rw-r--r-- 1 501 staff 275980 Apr 7 2015 fastafile.c

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._filez.py*

-rwxr-xr-x 1 501 staff 1712 Apr 7 2015 filez.py*

-rw-r--r-- 1 501 staff 399515 Apr 7 2015 htslibWrapper.c

-rwxr-xr-x 1 501 staff 35145 Apr 7 2015 LICENSE*

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._LICENSE*

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._platypusexceptions.py*

-rwxr-xr-x 1 501 staff 366 Apr 7 2015 platypusexceptions.py*

-rwxr-xr-x 1 501 staff 206 Apr 7 2015 ._Platypus.py*

-rwxr-xr-x 1 501 staff 1453 Apr 7 2015 Platypus.py*

-rw-r--r-- 1 501 staff 1007714 Apr 7 2015 platypusutils.c

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._pysam_util.c*

-rwxr-xr-x 1 501 staff 6185 Apr 7 2015 pysam_util.c*

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._pysam_util.h*

-rwxr-xr-x 1 501 staff 3184 Apr 7 2015 pysam_util.h*

-rwxr-xr-x 1 501 staff 15153 Apr 7 2015 README.txt*

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._runner.py*

-rwxr-xr-x 1 501 staff 29791 Apr 7 2015 runner.py*

-rwxr-xr-x 1 501 staff 206 Apr 7 2015 ._setup.py*

-rwxr-xr-x 1 501 staff 2881 Apr 7 2015 setup.py*

drwxr-xr-x 3 501 staff 4096 May 2 22:00 src/

drwxr-xr-x 2 501 staff 4096 May 2 22:00 tabix/

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._tabix_util.c*

-rwxr-xr-x 1 501 staff 70 Apr 7 2015 tabix_util.c*

-rwxr-xr-x 1 501 staff 487071 Apr 7 2015 TabProxies.c*

-rwxr-xr-x 1 501 staff 9554 Apr 7 2015 tandem.c*

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._tandem.h*

-rwxr-xr-x 1 501 staff 135 Apr 7 2015 tandem.h*

-rw-r--r-- 1 501 staff 515759 Apr 7 2015 variant.c

-rw-r--r-- 1 501 staff 1068275 Apr 7 2015 variantcaller.c

-rw-r--r-- 1 501 staff 602525 Apr 7 2015 variantFilter.c

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._variantutils.py*

-rwxr-xr-x 1 501 staff 7598 Apr 7 2015 variantutils.py*

-rwxr-xr-x 1 501 staff 212 Apr 7 2015 ._vcf.py*

-rwxr-xr-x 1 501 staff 46454 Apr 7 2015 vcf.py*

-rw-r--r-- 1 501 staff 1138010 Apr 7 2015 vcfutils.c

-rwxr-xr-x 1 501 staff 298 Apr 7 2015 ._window.py*

-rwxr-xr-x 1 501 staff 10885 Apr 7 2015 window.py*

I tried redownloading the Platypus tar from the website and rebuilt got an error during the build and variant caller is still not present.

x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/ctabix.o build/temp.linux-x86_64-2.7/tabix_util.o build/temp.linux-x86_64-2.7/tabix/bedidx.c.pysam.o build/temp.linux-x86_64-2.7/tabix/kstring.c.pysam.o build/temp.linux-x86_64-2.7/tabix/knetfile.c.pysam.o build/temp.linux-x86_64-2.7/tabix/index.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bgzip.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bgzf.c.pysam.o -lz -o build/lib.linux-x86_64-2.7/ctabix.so

building 'TabProxies' extension

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c TabProxies.c -o build/temp.linux-x86_64-2.7/TabProxies.o

building 'htslibWrapper' extension

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.linux-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC

htslibWrapper.c:243:25: fatal error: htslib/bgzf.h: No such file or directory

#include "htslib/bgzf.h"

compilation terminated.

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Setup failed. Check previous lines for errors

Has anyone encountered this or know of a solution?

With thanks,

Tim Wright

Biology, New Mexico State University

Matt Velinder

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Jul 30, 2018, 4:42:40 PM7/30/18

to Platypus Users

Hey Tim -

I also ran into this with my install and htslib.

I was able to fix it by doing the following:

Install htslib per the README.txt instructions.

Download and unzip Platypus

Copy htslib dir into the Platypus dir

$ cd ~/bin/Platypus_0.8.1/
$ cp -r ~/bin/htslib-1.9/htslib ./
$ ./buildPlatypus.sh