unable to start on mac

[christos proukakis]

Hello I would really like to use this, but
1) I am trying on a single core i7 mac with 16 G of RAM. Is there any chance it will work, even it takes days, or should I give up?
2) it doesnt wan to start- am i doing this the right way?

bash /Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh /SD/novoBreak_distribution_v1.1.3rc /Volumes/SD/bwa0712/hg19.fasta /Volumes/SD/MPS_work/P38_14.MB2.sorted.dup_removed.q40.bam /Volumes/Toshiba4Tb/WGSdata/mayo_MPS/P38_14.MB2.sorted.dup_removed.q40.chr4.sorted.bam 1 -PWD
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
readlink: illegal option -- f
usage: readlink [-n] [file ...]
usage: mkdir [-pv] [-m mode] directory ...
/Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 26: /novoBreak: No such file or directory
mkdir: group_reads: File exists
/Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 32: /samtools: No such file or directory
Can't open perl script "/group_bp_reads.pl": No such file or directory
(standard_in) 1: parse error
mkdir: split: File exists
awk: syntax error at source line 1
context is
{print > >>> int($1/rec)".txt" <<<
awk: illegal statement at source line 1
.txt
Can't open perl script "/run_ssake.pl": No such file or directory
mkdir: ssake: File exists
awk: can't open file ../group_reads/split/.ssake.asm.out
source line number 1
/Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 53: /bwa: No such file or directory
Can't open perl script "/infer_sv.pl": No such file or directory
(standard_in) 1: parse error
mkdir: split: File exists
x??
Can't open perl script "/infer_bp_v4.pl": No such file or directory
Can't open perl script "/filter_sv_icgc.pl": No such file or directory

[christos proukakis]

So i see that readlink is a problem, and i did
brew install coreutils
so i can use greadlink, and I edited the file changing readlink to greadlink everywhere

i also did brew install perl in case that was the problems

now I get someting to do with symlinks which someone commented on, probably beyond me to solve...

greadlink: invalid option -- 'P'
Try 'greadlink --help' for more information.
usage: mkdir [-pv] [-m mode] directory ...
/Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 26: -i: command not found
mkdir: group_reads: File exists
/Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 32: bam2fq: command not found
Can't open perl script "/group_bp_reads.pl": No such file or directory
(standard_in) 1: parse error
mkdir: split: File exists
awk: syntax error at source line 1
context is
{print > >>> int($1/rec)".txt" <<<
awk: illegal statement at source line 1
.txt
Can't open perl script "/run_ssake.pl": No such file or directory
mkdir: ssake: File exists
awk: can't open file ../group_reads/split/.ssake.asm.out
source line number 1
/Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 53: /bwa: No such file or directory
Can't open perl script "/infer_sv.pl": No such file or directory
(standard_in) 1: parse error
mkdir: split: File exists
x??
Can't open perl script "/infer_bp_v4.pl": No such file or directory
Can't open perl script "/filter_sv_icgc.pl": No such file or directory

[christos proukakis]

so I am also unable to run this on our main server Linux

any help will be very welcome!

bash novoBreak_distribution_v1.1.3rc/run_novoBreak.sh novoBreak_distribution_v1.1.3rc/novoBreak hg19.fasta bamfiles/P38_14.MB2.sorted.dup_removed.q40.bam bamfiles/P38_14CER.sorted.dup_removed.q40.bam 2 -PWD
readlink: invalid option -- 'P'
Try 'readlink --help' for more information.
mkdir: missing operand
Try 'mkdir --help' for more information.
novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 26: /home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/novoBreak: Not a directory
novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 32: /home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/samtools: Not a directory
Can't open perl script "/home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/group_bp_reads.pl": Not a directory
(standard_in) 1: syntax error
.txt
Can't open perl script "/home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/run_ssake.pl": Not a directory
awk: fatal: cannot open file `../group_reads/split/.ssake.asm.out' for reading (No such file or directory)
novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 53: /home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/bwa: Not a directory
Can't open perl script "/home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/infer_sv.pl": Not a directory
x??
Can't open perl script "/home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/infer_bp_v4.pl": Not a directory
Can't open perl script "/home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/filter_sv_icgc.pl": Not a directory