Trinity and jellyfish problem

[jevcampe]

Dear All,

When using Trinity, the pl script suddenly stops:

CMD: /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 766958445 both.fa
Can't exec "/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish": No such file or directory at Trinity.pl line 1472.
Error, cmd: /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 766958445 both.fa died with ret -1 at Trinity.pl line 1476.

Does anybody have any idea why?

Best wishes,

[peromhc]

you don't have jellyfish installed properly.

Did you execute the command 'make' inside the Trinity folder that you decompressed after downloading?

[jevcampe]

Yes I have, Everything gets installed properly however the error is still there.
Is there maybe a need to install jellyfish to?

[GenoMax]

Does the jellyfish file exist at the location referenced? Can you verify that?

$ ls -lt /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish

[jevcampe]

No
bin file is empty
$ ls -lt /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin
total 0

[GenoMax]

No
bin file is empty
$ ls -lt /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin
total 0

That does indicate that the plugin was not correctly compiled. Did you get any errors when you did the "make"? Can you try recompiling and post any errors you see.

[jevcampe]

Before doing this i would like to ask this:
Installing trinity is first unzipping the file followed by the command: make
Are there other parts I need to compile?

[jevcampe]

ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/bcftools'
make[3]: Entering directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
bam_tview.c:5:20: fatal error: curses.h: No such file or directory
compilation terminated.
make[2]: *** [bam_tview.o] Error 1
make[2]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam'
make[1]: *** [sam/libbam.a] Error 2
make[1]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3'
make: *** [all] Error 2

errors

[GenoMax]

Before doing this i would like to ask this:
Installing trinity is first unzipping the file followed by the command: make
Are there other parts I need to compile?

That is correct. I just verified that jellyfish gets built as part of the trinity compilation.

What OS are you using?

[GenoMax]

ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/bcftools'
make[3]: Entering directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
bam_tview.c:5:20: fatal error: curses.h: No such file or directory
compilation terminated.
make[2]: *** [bam_tview.o] Error 1
make[2]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam'
make[1]: *** [sam/libbam.a] Error 2
make[1]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3'
make: *** [all] Error 2

errors

You need to install "libncurses5-dev" library. If this is Ubuntu.

[jevcampe]

I'm using Linux version:
openSUSE 12.2 "mantis" - Kernel \r (\l)

[GenoMax]

I'm using Linux version:
openSUSE 12.2 "mantis" - Kernel \r (\l)

Then the library is likely called "ncurses-devel". Install that.

[sdriscoll]

Good old ncurses.

[jevcampe]

Hi all,

I have installed the package but the error still remains. However it looks that trinity has gone further compared to before.

-o bam2depth.o
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lcurses
collect2: error: ld returned 1 exit status
make[2]: *** [samtools] Error 1
make[2]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam'
make[1]: *** [sam/libbam.a] Error 2
make[1]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3'
make: *** [all] Error 2

[GenoMax]

Did you install "ncurses" library as well?