Unable to perform Quality Check - Mac OS X Yosemite 10.10.2

[DaleWatkins]

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 and gzip throwing up errors. The output of my run.log file is below. Any help/ideas would be fantastic. Thanks.

# /usr/local/opt/TRUP/bin/RTrace.pl --runlevel 1-4 --QC --sampleName CHI-0219 --seqType p --readlen 76 --trimedlen 76 --root ANALYSIS/ --anno $TRUP_Annot --readpool READS/ --species hg19 --readlen 76 --mapper gsnap --gf png --consisCount 5 --misPen 2 --uniqueBase 100 --WIG --RA 1 --threads 4 2>>run.log 

[2015/2/15 19:37:26]    ####### lane name is set to CHI-0219 #######

lanefile:       READS//CHI-0219_R1.fastq.gz
lanefile:       READS//CHI-0219_R2.fastq.gz

[2015/2/15 19:37:26]    ####### preparing directories #######

[2015/2/15 19:37:26]    mkdir -p ANALYSIS//CHI-0219/01_READS

[2015/2/15 19:37:26]    ln -s READS//CHI-0219_R1.fastq.gz ANALYSIS//CHI-0219/01_READS/CHI-0219_R1.fq.gz

[2015/2/15 19:37:26]    ln -s READS//CHI-0219_R2.fastq.gz ANALYSIS//CHI-0219/01_READS/CHI-0219_R2.fq.gz

[2015/2/15 19:37:26]    ####### runlevel 1 now #######

[2015/2/15 19:37:26]    gzip -d -c ANALYSIS//CHI-0219/01_READS/CHI-0219_R1.fq.gz | /usr/local/opt/TRUP/bin//fastx_quality_stats -Q33 -o ANALYSIS//CHI-0219/01_READS/CHI-0219_R1.fq.qc

sh: /usr/local/opt/TRUP/bin//fastx_quality_stats: cannot execute binary file
gzip: can't stat: ANALYSIS//CHI-0219/01_READS/CHI-0219_R1.fq.gz (ANALYSIS//CHI-0219/01_READS/CHI-0219_R1.fq.gz.gz): No such file or directory

[2015/2/15 19:37:26]    gzip -d -c ANALYSIS//CHI-0219/01_READS/CHI-0219_R2.fq.gz | /usr/local/opt/TRUP/bin//fastx_quality_stats -Q33 -o ANALYSIS//CHI-0219/01_READS/CHI-0219_R2.fq.qc

sh: /usr/local/opt/TRUP/bin//fastx_quality_stats: cannot execute binary file
gzip: can't stat: ANALYSIS//CHI-0219/01_READS/CHI-0219_R2.fq.gz (ANALYSIS//CHI-0219/01_READS/CHI-0219_R2.fq.gz.gz): No such file or directory
quality check finished, please check the quality file manually.

[DaleWatkins]

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?

[ruping]

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?

[DaleWatkins]

Hi ruping,

Thanks for getting back to me. I have bamtools 2.3.0 installed.