Open DaleWatkins opened 9 years ago
I have solved half the issue...
gzip
wasn't working because I wasn't specifying the full file PATH to the folder containing the FASTQ files, which was causing a broken symbolic link
error to occur. This has now been rectified.
My issue with the cannot execute binary file
error stills remains. This is occurring due to the TRUP binaries not being compatible with my system. I have tried running make
as follows, but am getting an error. This is what I am doing to install TRUP:
cd /usr/local/opt
git clone https://github.com/ruping/TRUP
Cloning into 'TRUP'...
remote: Counting objects: 802, done.
remote: Total 802 (delta 0), reused 0 (delta 0), pack-reused 802
Receiving objects: 100% (802/802), 48.52 MiB | 4.15 MiB/s, done.
Resolving deltas: 100% (537/537), done.
Checking connectivity... done.
cd TRUP/
make BAMTOOLS_ROOT=/usr/local/opt/bamtools/ ZLIB_ROOT=/usr/local/Cellar/zlib/1.2.8/
* compiling Rseq_bam_stats.cpp
In file included from ./src/Rseq_bam_stats.cpp:28:
/usr/local/opt/bamtools//include/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/usr/local/opt/bamtools//include/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/usr/local/opt/bamtools//include/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/usr/local/opt/bamtools//include/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/usr/local/opt/bamtools//include/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/usr/local/opt/bamtools//include/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Rseq_bam_stats] Error 1
Any ideas of what I'm doing wrong?
Hi DaleWatkins,
There seems to be two issues, first is that the binaries I included in the package is not compatible for MAC OS, this I will take care and update. Will let you know once finished.
The second is that the bamtools library seems to be different from what I was using, Which version of bamtools api are you using?
Hi ruping,
Thanks for getting back to me. I have bamtools 2.3.0 installed.
Hi, I'm trying to use TRUP to identify fusions in my RNAseq data, using my 64-bit Mac OS X Yosemite 10.10.2. I have an issue performing the initial Quality Check, with both
fastx_quality_stats
andgzip
throwing up errors. The output of my run.log file is below. Any help/ideas would be fantastic. Thanks.