Re: [Transdecoder-users] transdecoder ffindex error

[Brian H. <bh...@br...>]

Hi Eric,

Try this too:

  make cdhit

and then run the sample data.

best,

~brian


On Thu, May 1, 2014 at 9:16 AM, ERIC WAFULA <ek...@ps...> wrote:

> 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...
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas