Re: [Transdecoder-users] transdecoder ffindex error
Extracting likely coding regions from transcript sequences
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Re: [Transdecoder-users] transdecoder ffindex error
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From: Brian H. <bh...@br...> - 2014-05-01 17:19:18
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Great! Thanks for the update! ~b On Thu, May 1, 2014 at 1:07 PM, ERIC WAFULA <ek...@ps...> wrote: > 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.pltransdecoder.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... >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get >>>>> unparalleled scalability from the best Selenium testing platform >>>>> available. >>>>> Simple to use. Nothing to install. Get started now for free." >>>>> http://p.sf.net/sfu/SauceLabs >>>>> _______________________________________________ >>>>> Transdecoder-users mailing list >>>>> Tra...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/transdecoder-users >>>>> >>>>> >>>> >>>> >>>> -- >>>> -- >>>> 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... > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
