Re: [Transdecoder-users] transdecoder ffindex error

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

Brian,

Thanks very much! That solved the problem.
TransDecoder now running okay.

Eric


On Thu, May 1, 2014 at 11:18 AM, Brian Haas <bh...@br...>wrote:

> 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.pltransdecoder.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
>
>
>



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