Re: [Transdecoder-users] transdecoder ffindex error

[ERIC W. <ek...@ps...>]

Brian

I am building on linux machine (centos 5.8).
"make parafly" completed okay, but i get an error mesaage when running
running the test script. something to do cd

 [ekw10@comandra sample_data]$ ./runMe.sh

-parsing cufflinks output: transcripts.gtf

-parsing genome fasta: test.genome.fasta

-done parsing genome.

// processing 7000000090838467

CMD:
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/util/
get_top_longest_fasta_entries.pl transdecoder.tmp.nopfam/longest_orfs.cds
2000 > transdecoder.tmp.nopfam/redundant_top

CMD:
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/util/bin/cd-hit-est
-r 1 -i transdecoder.tmp.nopfam/redundant_top -o
transdecoder.tmp.nopfam/redundant_top.nr90 -M 0 -T 2 >/dev/null 2>/dev/null

*Error, cmd:
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/util/bin/cd-hit-est
-r 1 -i transdecoder.tmp.nopfam/redundant_top -o
transdecoder.tmp.nopfam/redundant_top.nr90 -M 0 -T 2 >/dev/null 2>/dev/null
died with ret 256 at ../TransDecoder line 498.*


I aslo tried with my own dataset, and am getting the folllowing error:

ekw10@comandra assembly]$
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/TransDecoder
-t OrAe0GB1.fasta

CMD:
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/util/
get_top_longest_fasta_entries.pl transdecoder.tmp.28440/longest_orfs.cds
2000 > transdecoder.tmp.28440/redundant_top

CMD:
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/util/bin/cd-hit-est
-r 1 -i transdecoder.tmp.28440/redundant_top -o
transdecoder.tmp.28440/redundant_top.nr90 -M 0 -T 2 >/dev/null 2>/dev/null

E*rror, cmd:
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/util/bin/cd-hit-est
-r 1 -i transdecoder.tmp.28440/redundant_top -o
transdecoder.tmp.28440/redundant_top.nr90 -M 0 -T 2 >/dev/null 2>/dev/null
died with ret 256 at
/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/TransDecoder
line 498. *


*Eric*


On Wed, Apr 30, 2014 at 9:41 PM, Brian Haas <bh...@br...>wrote:

> Hi Eric,
>
> Are you building this on linux or mac?  If mac, I've never gotten ffindex
> to build on mac - only linux.
>
> In any case, you can use transdecoder without using the ffindex.  You can
> try
>
>    make parafly
>
> and then
>
>   cd sample_data && runMe.sh
>
> and see if it works.
>
> best,
>
> ~brian
>
>
>
> On Wed, Apr 30, 2014 at 6:30 PM, ERIC WAFULA <ek...@ps...> wrote:
>
>> Hi Brian,
>>
>> I tried for days now install transdecoder without success. I keep getting
>> ffindex error to do with some kind of incompatabilty.
>>
>> sudo make
>>
>> if [[ ! -s pfam/Pfam-AB.hmm.bin ]]; then echo "Downloading PFAM database"
>> && wget '
>> http://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin/download'
>> -O pfam/Pfam-AB.hmm.bin; fi
>>
>> if [[ ! -e pfam/Pfam-AB.hmm.bin.h3i ]]; then echo "Preparing PFAM
>> database" && hmmpress pfam/Pfam-AB.hmm.bin; fi
>>
>> cd 3rd_party/ffindex && make HAVE_MPI=1 && make install
>> INSTALL_DIR=../../../util HAVE_MPI=1
>>
>> make[1]: Entering directory
>> `/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3'
>>
>> make -C src -f Makefile all
>>
>> make[2]: Entering directory
>> `/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3/src'
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffindex_apply.o ffindex_apply.c
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffindex.o ffindex.c
>>
>> ffindex.c: In function 'ffindex_tree_write':
>>
>> ffindex.c:518: warning: ISO C forbids nested functions
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffutil.o ffutil.c
>>
>> gcc -fopenmp -Wl,-z,defs -shared -Wl,-soname,libffindex.so.0.1 -o
>> libffindex.so.0.1 ffindex.o ffutil.o -lc
>>
>> ln -sf libffindex.so.0.1 libffindex.so
>>
>> gcc -fopenmp -lffindex -L.  ffindex_apply.o libffindex.so
>> libffindex.so.0.1 ffindex.h   -o ffindex_apply
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffindex_from_fasta.o ffindex_from_fasta.c
>>
>> gcc -fopenmp -o ffindex_from_fasta ffindex_from_fasta.o -lffindex -L. -L.
>> -lffindex
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffindex_get.o ffindex_get.c
>>
>> gcc -fopenmp -o ffindex_get ffindex_get.o -lffindex -L. -L. -lffindex
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffindex_build.o ffindex_build.c
>>
>> gcc -fopenmp -o ffindex_build ffindex_build.o -lffindex -L. -L. -lffindex
>>
>> gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c
>> -o ffindex_modify.o ffindex_modify.c
>>
>> gcc -fopenmp -o ffindex_modify ffindex_modify.o -lffindex -L. -L.
>> -lffindex
>>
>> ar rcs libffindex.a ffutil.o ffindex.o
>>
>> gcc -fopenmp -o ffindex_unpack ffindex_unpack.o -lffindex -L. -L.
>> -lffindex
>>
>> mpicc -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -c
>> ffindex_apply_mpi.c -o ffindex_apply_mpi.o
>>
>> ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry':
>>
>> ffindex_apply_mpi.c:151: warning: format '%ld' expects type 'long int',
>> but argument 4 has type 'size_t'
>>
>> ffindex_apply_mpi.c:151: warning: format '%ld' expects type 'long int',
>> but argument 5 has type 'size_t'
>>
>> mpicc -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -o
>> ffindex_apply_mpi  ffindex_apply_mpi.o -lffindex -L.
>>
>> */usr/bin/ld: skipping incompatible ./libffindex.so when searching for
>> -lffindex*
>>
>> */usr/bin/ld: skipping incompatible ./libffindex.a when searching for
>> -lffindex*
>>
>> */usr/bin/ld: cannot find -lffindex*
>>
>> *collect2: ld returned 1 exit status*
>>
>> *make[2]: *** [ffindex_apply_mpi] Error 1*
>>
>> *make[2]: Leaving directory
>> `/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3/src'*
>>
>> *make[1]: *** [all] Error 2*
>>
>> *make[1]: Leaving directory
>> `/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3'*
>>
>> *make: *** [ffindex] Error 2*
>>
>> Thanks for your help.
>>
>> Eric
>>
>>
>> --
>> Eric Kenneth Wafula
>> Bioinformatics Programmer
>> Claude dePamphilis Lab
>> Department of Biology
>> Penn State University
>> 814-865-2449
>> ek...@ps...
>>
>>
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>>
>>
>
>
> --
> --
> Brian J. Haas
> The Broad Institute
> http://broad.mit.edu/~bhaas
>
>
>



-- 
Eric Kenneth Wafula
Bioinformatics Programmer
Claude dePamphilis Lab
Department of Biology
Penn State University
814-865-2449
ek...@ps...