transdecoder-users Mailing List for TranscriptDecoder (Page 5)
Extracting likely coding regions from transcript sequences
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From: <Ale...@cs...> - 2014-02-20 01:39:43
|
Hello Sorry to hear about that, sounds like a sysadmin issue. What does your HPC system administrator say? Can /they/ run ffindex_apply_mpi using any command (see READ)? From: Simen Rød Sandve [mailto:sim...@nm...] Sent: Wednesday, February 19, 2014 19:50 PM To: tra...@li... Subject: [Transdecoder-users] Transdecoder error - cannot allocate memory Hello, I am trying to run transcoder with MPI on our cluster. However, the script seems to fail about 50% of the cases. The error message I get is «ERROR in fork() 10: Cannot allocate memory» (see attaches slurm-file for entire error message output). Im running the script on a small subset of sequences (100) and we have plenty full of computer resources (200 nodes and 2 TB memory), hence memory shouldn't be a problem. I would be very grateful if you had some ideas of what could be the cause of the failed transcoder runs. Best Simen ________________________________ Simen R. Sandve, PhD Researcher IHA/NMBU +47 64965554 ________________________________ |
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From: Simen R. S. <sim...@nm...> - 2014-02-19 09:06:35
|
Hello, I am trying to run transcoder with MPI on our cluster. However, the script seems to fail about 50% of the cases. The error message I get is «ERROR in fork() 10: Cannot allocate memory» (see attaches slurm-file for entire error message output). Im running the script on a small subset of sequences (100) and we have plenty full of computer resources (200 nodes and 2 TB memory), hence memory shouldn't be a problem. I would be very grateful if you had some ideas of what could be the cause of the failed transcoder runs. Best Simen ________________________________ Simen R. Sandve, PhD Researcher IHA/NMBU +47 64965554 ________________________________ |
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From: <Ale...@cs...> - 2014-02-17 21:59:30
|
Sorry not a mac fan.
--
Alexie Papanicolaou
CSIRO Ecosystem Sciences
________________________________
From: Brian Haas
Sent: Monday, 17 February 2014 6:22:53 PM
To: Dorsey, Brian
Cc: tra...@li...; Papanicolaou, Alexie (CES, Black Mountain)
Subject: Re: [Transdecoder-users] Two compilation errors on OSX
Hi Brian,
I think it works well on linux, but I'm not sure it works 'out of the box' on mac.
Alexie might have more to say here.
best,
~b
On Fri, Feb 7, 2014 at 5:54 PM, Dorsey, Brian <bd...@hu...<mailto:bd...@hu...>> wrote:
Hello decoders,
I got the following message when trying to compile transdecoder on Mac OSX 10.7.5:
sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make
make[3]: *** No targets specified and no makefile found. Stop.
make[2]: *** [ext/fmemopen.o] Error 2
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2
The makefile in /ext is named "Makefile.osx", so I changed: /transdecoder_rel16JAN2014/3rd_party/ffindex/src/Makefile.osx line 11 from "cd ext && make" to "cd ext && make -f Makefile.osx"
This fixed the first error but...
Then I get this error:
sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make -f Makefile.osx
cc -std=c99 -O3 -g -fPIC -Wall -c -o fmemopen.o fmemopen.c
cc -std=c99 -O3 -g -fPIC -Wall -fnested-functions -c -o ffindex.o ffindex.c
clang: warning: argument unused during compilation: '-fnested-functions'
ffindex.c:517:68: error: expected ';' at end of declaration
void action(const void *node, const VISIT which, const int depth)
^
;
1 error generated.
make[2]: *** [ffindex.o] Error 1
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2
Below is the block in /transdecoder_rel16JAN2014/3rd_party/ffindex/src/ffindex.c referenced above:
int ffindex_tree_write(ffindex_index_t* index, FILE* index_file)
{
int ret = EXIT_SUCCESS;
void action(const void *node, const VISIT which, const int depth)
{
ffindex_entry_t *entry;
switch (which)
{
case preorder:
break;
case endorder:
break;
case postorder:
case leaf:
entry = *(ffindex_entry_t **) node;
if(fprintf(index_file, "%s\t%zd\t%zd\n", entry->name, entry->offset, entry->length) < 0)
ret = EXIT_FAILURE;
break;
}
}
twalk(index->tree_root, action);
return ret;
}
This one I'm not comfortable trying to fix myself.
I know zero about c programming but it doesn't seem there should be a ';' at the end of this line.
However, should I put one there or is there another problem to address?
Thanks for any help,
Brian D.
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brian Dorsey, Ph.D.
Post-Doctoral Research Associate
The Huntington Botanical Gardens
bd...@hu...<mailto:bd...@hu...>
------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience. Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
Transdecoder-users mailing list
Tra...@li...<mailto:Tra...@li...>
https://lists.sourceforge.net/lists/listinfo/transdecoder-users
--
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas
|
|
From: Brian H. <bh...@br...> - 2014-02-17 18:23:00
|
Hi Brian,
I think it works well on linux, but I'm not sure it works 'out of the box'
on mac.
Alexie might have more to say here.
best,
~b
On Fri, Feb 7, 2014 at 5:54 PM, Dorsey, Brian <bd...@hu...>wrote:
> Hello decoders,
>
> I got the following message when trying to compile transdecoder on Mac OSX
> 10.7.5:
>
> sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
> cd 3rd_party/ffindex && make HAVE_MPI=1 && make install
> INSTALL_DIR=../../../util HAVE_MPI=1
> make -C src -f Makefile.osx all
> cd ext && make
> make[3]: *** No targets specified and no makefile found. Stop.
> make[2]: *** [ext/fmemopen.o] Error 2
> make[1]: *** [all] Error 2
> make: *** [ffindex] Error 2
>
>
> The makefile in /ext is named "Makefile.osx", so I changed:
> /transdecoder_rel16JAN2014/3rd_party/ffindex/src/Makefile.osx line 11 from
> "cd ext && make" to "cd ext && make -f Makefile.osx"
>
> This fixed the first error but...
>
> Then I get this error:
>
> sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
> cd 3rd_party/ffindex && make HAVE_MPI=1 && make install
> INSTALL_DIR=../../../util HAVE_MPI=1
> make -C src -f Makefile.osx all
> cd ext && make -f Makefile.osx
> cc -std=c99 -O3 -g -fPIC -Wall -c -o fmemopen.o fmemopen.c
> cc -std=c99 -O3 -g -fPIC -Wall -fnested-functions -c -o ffindex.o
> ffindex.c
> clang: warning: argument unused during compilation: '-fnested-functions'
> ffindex.c:517:68: error: expected ';' at end of declaration
> void action(const void *node, const VISIT which, const int depth)
> ^
> ;
> 1 error generated.
> make[2]: *** [ffindex.o] Error 1
> make[1]: *** [all] Error 2
> make: *** [ffindex] Error 2
>
>
> Below is the block in
> /transdecoder_rel16JAN2014/3rd_party/ffindex/src/ffindex.c referenced above:
>
> int ffindex_tree_write(ffindex_index_t* index, FILE* index_file)
> {
> int ret = EXIT_SUCCESS;
> void action(const void *node, const VISIT which, const int depth)
> {
> ffindex_entry_t *entry;
> switch (which)
> {
> case preorder:
> break;
> case endorder:
> break;
> case postorder:
> case leaf:
> entry = *(ffindex_entry_t **) node;
> if(fprintf(index_file, "%s\t%zd\t%zd\n", entry->name,
> entry->offset, entry->length) < 0)
> ret = EXIT_FAILURE;
> break;
> }
> }
> twalk(index->tree_root, action);
> return ret;
> }
>
> This one I'm not comfortable trying to fix myself.
> I know zero about c programming but it doesn't seem there should be a ';'
> at the end of this line.
> However, should I put one there or is there another problem to address?
>
> Thanks for any help,
> Brian D.
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Brian Dorsey, Ph.D.
> Post-Doctoral Research Associate
> The Huntington Botanical Gardens
> bd...@hu...
>
>
>
>
>
> ------------------------------------------------------------------------------
> Android apps run on BlackBerry 10
> Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> Now with support for Jelly Bean, Bluetooth, Mapview and more.
> Get your Android app in front of a whole new audience. Start now.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
|
|
From: Brian H. <bh...@br...> - 2014-02-14 04:22:50
|
Hi Will, Can you try using the latest version of the code from sourceforge? Much has changed. If it still doesn't work, we can look into the latest code and try to address it. best, ~brian On Thu, Feb 13, 2014 at 7:54 PM, Will Jackson <wil...@gm...>wrote: > Hi guys, > I am trying to run cdna_alignment_orf_to_genome_orf.pl but am getting > this error: > > Use of uninitialized value $info in pattern match (m//) at > /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ > cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. > Use of uninitialized value $info in concatenation (.) or string at > /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ > cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. > Error, cannot parse ID from at > /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ > cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. > > As inputs I am using are: > GFF3 file produced by transdecoder of transcripts produced by the PASA > annotation comparison and update process. > I used bedtools getfasta -name to get the fasta sequences for the > transcripts produced by PASA. I then ran them through transdecoder to get > the cds and gff3 files, then I used the seqclean utility from trinity to > remove some (195) low quality ORFs. > > The 'transcripts.gff3' file (2nd positional argument) I am using is the > one produced by PASA annotation comparison and update. > > Below is the head of each file: > $ head GG_MAKER_UPDATE_ORFs.transdecoder.gff3 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . gene 315 1454 . - . > ID=g.59;Name=ORF%20g.59%20m.59%20type%3Acomplete%20len%3A380%20%28-%29 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . mRNA 315 1454 . - . ID=m.59;Parent=g.59 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . exon 315 1454 . - . > ID=m.59.exon1;Parent=m.59 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . CDS 315 1454 . - . > ID=cds.m.59;Parent=m.59 > > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . gene 1570 2298 . - . > ID=g.60;Name=ORF%20g.60%20m.60%20type%3Acomplete%20len%3A243%20%28-%29 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . mRNA 1570 2298 . - . ID=m.60;Parent=g.60 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . exon 1570 2298 . - . > ID=m.60.exon1;Parent=m.60 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . CDS 1570 2298 . - . > ID=cds.m.60;Parent=m.60 > > head APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3 > ==> APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3 > <== > # ORIGINAL: genemark-scaffold_1446-processed-gene-0.1-mRNA-1 original gene > structure, not modified by PASA > scaffold_1446 maker gene 6232 6658 . - . > ID=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1 > scaffold_1446 maker mRNA 6232 6658 . - . > ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1 > scaffold_1446 maker exon 6617 6658 . - . > ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > scaffold_1446 maker CDS 6617 6658 . - 0 > ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > scaffold_1446 maker exon 6232 6534 . - . > ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon2;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > scaffold_1446 maker CDS 6232 6534 . - 0 > ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > > > #PROT genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > genemark-scaffold_1446-processed-gene-0.1 > MDAEDTRSALIWWKERQGKYPILSSLARDYLACSASSCAAERTFSAAADVCPGNRGKLLPRTIEMCVSSRMWLKDKVPVTGDFEAANNIVQKFTAFKEKNRLNTIDPSPDITKK* > > >m.60 g.60 ORF g.60 m.60 type:complete len:243 (-) > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18:1570-2298(-) > ATGACCAAACCGTGCGTTCATAATCCCCTCAATTCGTCTCGCCTTGATTCTACGCCTCAG > TTGACAGGATTATACGTGTTGTCACCGAACTTCATCATCTCTAAATATAAGATTACTCAA > TATGACCTTTCGAACGTGTCCACCATACAAAATGCCGCATCAGATTCATTATCCGTCGAT > CCTTCACATCGCCCCATGCCTGGCACAAGATCTCGTGGAGGAGGCGGGGATATGTCATTG > GATCCTCCCATCTCGACTAGCAATGAGAAACCGGTATTGACAAAAAAGTCGAGCATCATT > TTCCCAGTCCCTGTAAATCACTGTAGCATCAGTCCAGACTCAAAATCGATGGTGGCCGTA > GGCGATAGTAGCGAAGTGTTTATATATGACTGTCAAAATGCACATCAATCAAATGAACCG > TTGGTTGGCGATTGGCGATTGGGTCCTCGAAAGATTCATTTACCTGGGGTTTCGCCTCTC > ACCGGTAGCTTTAGTACGAGCTGGAATCAGTATGGAGATAAATTTGCAGTCGCAAGTGAG > > > Am I doing something wrong? > > Thanks > Will > > > > > ------------------------------------------------------------------------------ > Android apps run on BlackBerry 10 > Introducing the new BlackBerry 10.2.1 Runtime for Android apps. > Now with support for Jelly Bean, Bluetooth, Mapview and more. > Get your Android app in front of a whole new audience. Start now. > > http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk > _______________________________________________ > 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 |
|
From: Will J. <wil...@gm...> - 2014-02-14 00:55:02
|
Hi guys, I am trying to run cdna_alignment_orf_to_genome_orf.pl but am getting this error: Use of uninitialized value $info in pattern match (m//) at /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. Use of uninitialized value $info in concatenation (.) or string at /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. Error, cannot parse ID from at /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. As inputs I am using are: GFF3 file produced by transdecoder of transcripts produced by the PASA annotation comparison and update process. I used bedtools getfasta -name to get the fasta sequences for the transcripts produced by PASA. I then ran them through transdecoder to get the cds and gff3 files, then I used the seqclean utility from trinity to remove some (195) low quality ORFs. The 'transcripts.gff3' file (2nd positional argument) I am using is the one produced by PASA annotation comparison and update. Below is the head of each file: $ head GG_MAKER_UPDATE_ORFs.transdecoder.gff3 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . gene 315 1454 . - . ID=g.59;Name=ORF%20g.59%20m.59%20type%3Acomplete%20len%3A380%20%28-%29 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . mRNA 315 1454 . - . ID=m.59;Parent=g.59 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . exon 315 1454 . - . ID=m.59.exon1;Parent=m.59 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . CDS 315 1454 . - . ID=cds.m.59;Parent=m.59 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . gene 1570 2298 . - . ID=g.60;Name=ORF%20g.60%20m.60%20type%3Acomplete%20len%3A243%20%28-%29 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . mRNA 1570 2298 . - . ID=m.60;Parent=g.60 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . exon 1570 2298 . - . ID=m.60.exon1;Parent=m.60 ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 . CDS 1570 2298 . - . ID=cds.m.60;Parent=m.60 head APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3 ==> APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3 <== # ORIGINAL: genemark-scaffold_1446-processed-gene-0.1-mRNA-1 original gene structure, not modified by PASA scaffold_1446 maker gene 6232 6658 . - . ID=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1 scaffold_1446 maker mRNA 6232 6658 . - . ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1 scaffold_1446 maker exon 6617 6658 . - . ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 scaffold_1446 maker CDS 6617 6658 . - 0 ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 scaffold_1446 maker exon 6232 6534 . - . ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon2;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 scaffold_1446 maker CDS 6232 6534 . - 0 ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 #PROT genemark-scaffold_1446-processed-gene-0.1-mRNA-1 genemark-scaffold_1446-processed-gene-0.1 MDAEDTRSALIWWKERQGKYPILSSLARDYLACSASSCAAERTFSAAADVCPGNRGKLLPRTIEMCVSSRMWLKDKVPVTGDFEAANNIVQKFTAFKEKNRLNTIDPSPDITKK* >m.60 g.60 ORF g.60 m.60 type:complete len:243 (-) ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18:1570-2298(-) ATGACCAAACCGTGCGTTCATAATCCCCTCAATTCGTCTCGCCTTGATTCTACGCCTCAG TTGACAGGATTATACGTGTTGTCACCGAACTTCATCATCTCTAAATATAAGATTACTCAA TATGACCTTTCGAACGTGTCCACCATACAAAATGCCGCATCAGATTCATTATCCGTCGAT CCTTCACATCGCCCCATGCCTGGCACAAGATCTCGTGGAGGAGGCGGGGATATGTCATTG GATCCTCCCATCTCGACTAGCAATGAGAAACCGGTATTGACAAAAAAGTCGAGCATCATT TTCCCAGTCCCTGTAAATCACTGTAGCATCAGTCCAGACTCAAAATCGATGGTGGCCGTA GGCGATAGTAGCGAAGTGTTTATATATGACTGTCAAAATGCACATCAATCAAATGAACCG TTGGTTGGCGATTGGCGATTGGGTCCTCGAAAGATTCATTTACCTGGGGTTTCGCCTCTC ACCGGTAGCTTTAGTACGAGCTGGAATCAGTATGGAGATAAATTTGCAGTCGCAAGTGAG Am I doing something wrong? Thanks Will |
|
From: Dorsey, B. <bd...@hu...> - 2014-02-10 19:08:47
|
Hello decoders,
Sorry if this is a duplicate post, the first attempt was before subscribing to the list.
I got the following message when trying to compile transdecoder on Mac OSX 10.7.5:
sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make
make[3]: *** No targets specified and no makefile found. Stop.
make[2]: *** [ext/fmemopen.o] Error 2
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2
The makefile in /ext is named "Makefile.osx", so I changed: /transdecoder_rel16JAN2014/3rd_party/ffindex/src/Makefile.osx line 11 from "cd ext && make" to "cd ext && make -f Makefile.osx"
This fixed the first error but...
Then I get this error:
sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make -f Makefile.osx
cc -std=c99 -O3 -g -fPIC -Wall -c -o fmemopen.o fmemopen.c
cc -std=c99 -O3 -g -fPIC -Wall -fnested-functions -c -o ffindex.o ffindex.c
clang: warning: argument unused during compilation: '-fnested-functions'
ffindex.c:517:68: error: expected ';' at end of declaration
void action(const void *node, const VISIT which, const int depth)
^
;
1 error generated.
make[2]: *** [ffindex.o] Error 1
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2
Below is the block in /transdecoder_rel16JAN2014/3rd_party/ffindex/src/ffindex.c referenced above:
int ffindex_tree_write(ffindex_index_t* index, FILE* index_file)
{
int ret = EXIT_SUCCESS;
void action(const void *node, const VISIT which, const int depth)
{
ffindex_entry_t *entry;
switch (which)
{
case preorder:
break;
case endorder:
break;
case postorder:
case leaf:
entry = *(ffindex_entry_t **) node;
if(fprintf(index_file, "%s\t%zd\t%zd\n", entry->name, entry->offset, entry->length) < 0)
ret = EXIT_FAILURE;
break;
}
}
twalk(index->tree_root, action);
return ret;
}
This one I'm not comfortable trying to fix myself.
I know zero about c programming but it doesn't seem there should be a ';' at the end of this line.
However, should I put one there or is there another problem to address?
Thanks for any help,
Brian D.
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brian Dorsey, Ph.D.
Post-Doctoral Research Associate
The Huntington Botanical Gardens
bd...@hu...
|
|
From: Dorsey, B. <bd...@hu...> - 2014-02-07 23:08:47
|
Hello decoders,
I got the following message when trying to compile transdecoder on Mac OSX 10.7.5:
sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make
make[3]: *** No targets specified and no makefile found. Stop.
make[2]: *** [ext/fmemopen.o] Error 2
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2
The makefile in /ext is named "Makefile.osx", so I changed: /transdecoder_rel16JAN2014/3rd_party/ffindex/src/Makefile.osx line 11 from "cd ext && make" to "cd ext && make -f Makefile.osx"
This fixed the first error but...
Then I get this error:
sn01564:transdecoder_rel16JAN2014 bdorsey$ make nopfam
cd 3rd_party/ffindex && make HAVE_MPI=1 && make install INSTALL_DIR=../../../util HAVE_MPI=1
make -C src -f Makefile.osx all
cd ext && make -f Makefile.osx
cc -std=c99 -O3 -g -fPIC -Wall -c -o fmemopen.o fmemopen.c
cc -std=c99 -O3 -g -fPIC -Wall -fnested-functions -c -o ffindex.o ffindex.c
clang: warning: argument unused during compilation: '-fnested-functions'
ffindex.c:517:68: error: expected ';' at end of declaration
void action(const void *node, const VISIT which, const int depth)
^
;
1 error generated.
make[2]: *** [ffindex.o] Error 1
make[1]: *** [all] Error 2
make: *** [ffindex] Error 2
Below is the block in /transdecoder_rel16JAN2014/3rd_party/ffindex/src/ffindex.c referenced above:
int ffindex_tree_write(ffindex_index_t* index, FILE* index_file)
{
int ret = EXIT_SUCCESS;
void action(const void *node, const VISIT which, const int depth)
{
ffindex_entry_t *entry;
switch (which)
{
case preorder:
break;
case endorder:
break;
case postorder:
case leaf:
entry = *(ffindex_entry_t **) node;
if(fprintf(index_file, "%s\t%zd\t%zd\n", entry->name, entry->offset, entry->length) < 0)
ret = EXIT_FAILURE;
break;
}
}
twalk(index->tree_root, action);
return ret;
}
This one I'm not comfortable trying to fix myself.
I know zero about c programming but it doesn't seem there should be a ';' at the end of this line.
However, should I put one there or is there another problem to address?
Thanks for any help,
Brian D.
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brian Dorsey, Ph.D.
Post-Doctoral Research Associate
The Huntington Botanical Gardens
bd...@hu...
|
|
From: <Ale...@cs...> - 2014-02-01 00:11:37
|
It is possible that we find more than ORF in a contig - is there a reason you think that a mRNA assembly ought to be forced to only have one ORF? It is rare but assemblies can fuse genes. Would you prefer if the smaller ORF was not printed out (and therefore you wouldn't have the option of checking if it is real) ? It is interesting that the name is the same. I guess this is not a Trinity assembly? Brian? ________________________________ From: Zhang, Ning [Zh...@si...] Sent: Saturday, 1 February 2014 2:01 AM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: <tra...@li...> Subject: Re: [Transdecoder-users] problems of installation Yes, the name is identical, but the sequence is different. Something like that: >Ampelocissus_ele_scaffold99_Locus_33_4_22.4 MGQKNSTHSTMEENCKWHKLLPRERERLMGTVGRRAIRSKLKNCRAMEVGIAATIRDQNG TD* >Ampelocissus_ele_scaffold99_Locus_33_4_22.4 MDRQNSFHESFPRSYRGKQFPFLQGPNPILPGTSVCQPLLDPSSASGNGSGGQKMFSDGL NRVISSDRALSLLSSPLPETQEIGLSSMVQQNPIPPAQTLIPSLHYTGLSQYASSQGMGD SVGSILVSDGSSNANLHCPAIFQLGPDGSSTNSSHQTLSFSWE* There are many cases in my .pep file. Ning On Jan 30, 2014, at 8:06 PM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: Are they duplicate (two identical proteins) from one contig or two proteins (different coordinates) in a contig? A -- Alexie Papanicolaou CSIRO Ecosystem Sciences ________________________________ From: Zhang, Ning Sent: Thursday, 30 January 2014 9:56:19 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: <tra...@li...<mailto:tra...@li...>> Subject: Re: [Transdecoder-users] problems of installation Hi, all: I found that there are some duplicate peptides in *.transdecoder.pep. What happened? How can I get only one peptide for each contig, maybe the longest one. Thanks Ning On Jan 25, 2014, at 7:55 AM, Zhang, Ning wrote: yes, I made it. After installing this module, it works. If you use Transdecoder on cluster, you had better install the module at your own path. A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help. Ning On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: It seems that you or your sysadmin will have to install the perl module: $ cpan URI::Escape If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle... a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744> -- ResearcherID<https://urldefense.proofpoint.com/v1/url?u=http://www.researcherid.com/rid/A-1618-2011&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=5b2d419ad1f31ad2bbaadeb5d7c6b74bd08888dd929ae8933194347cc2dd0d3e> -- Bioinformatics is also an experimental science ________________________________ From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>] Sent: Saturday, 25 January 2014 6:06 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] problems of installation Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrk&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=d5aa942dbe90f9c4cee4ace02d5ae1325472ee07cfbb022ee55849276e387cdb_______________________________________________ Transdecoder-users mailing list Tra...@li...<mailto:Tra...@li...> https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/transdecoder-users&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=8c9eb782b20a3b7360b0edc5a5b5bc9fec97c9de3a1f28a000673bb1f01d8bae |
|
From: Zhang, N. <Zh...@si...> - 2014-01-31 15:02:07
|
Yes, the name is identical, but the sequence is different. Something like that: >Ampelocissus_ele_scaffold99_Locus_33_4_22.4 MGQKNSTHSTMEENCKWHKLLPRERERLMGTVGRRAIRSKLKNCRAMEVGIAATIRDQNG TD* >Ampelocissus_ele_scaffold99_Locus_33_4_22.4 MDRQNSFHESFPRSYRGKQFPFLQGPNPILPGTSVCQPLLDPSSASGNGSGGQKMFSDGL NRVISSDRALSLLSSPLPETQEIGLSSMVQQNPIPPAQTLIPSLHYTGLSQYASSQGMGD SVGSILVSDGSSNANLHCPAIFQLGPDGSSTNSSHQTLSFSWE* There are many cases in my .pep file. Ning On Jan 30, 2014, at 8:06 PM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: Are they duplicate (two identical proteins) from one contig or two proteins (different coordinates) in a contig? A -- Alexie Papanicolaou CSIRO Ecosystem Sciences ________________________________ From: Zhang, Ning Sent: Thursday, 30 January 2014 9:56:19 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: <tra...@li...<mailto:tra...@li...>> Subject: Re: [Transdecoder-users] problems of installation Hi, all: I found that there are some duplicate peptides in *.transdecoder.pep. What happened? How can I get only one peptide for each contig, maybe the longest one. Thanks Ning On Jan 25, 2014, at 7:55 AM, Zhang, Ning wrote: yes, I made it. After installing this module, it works. If you use Transdecoder on cluster, you had better install the module at your own path. A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help. Ning On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: It seems that you or your sysadmin will have to install the perl module: $ cpan URI::Escape If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle... a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744> -- ResearcherID<https://urldefense.proofpoint.com/v1/url?u=http://www.researcherid.com/rid/A-1618-2011&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=5b2d419ad1f31ad2bbaadeb5d7c6b74bd08888dd929ae8933194347cc2dd0d3e> -- Bioinformatics is also an experimental science ________________________________ From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>] Sent: Saturday, 25 January 2014 6:06 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] problems of installation Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrk&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=d5aa942dbe90f9c4cee4ace02d5ae1325472ee07cfbb022ee55849276e387cdb_______________________________________________ Transdecoder-users mailing list Tra...@li...<mailto:Tra...@li...> https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/transdecoder-users&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=8c9eb782b20a3b7360b0edc5a5b5bc9fec97c9de3a1f28a000673bb1f01d8bae |
|
From: <Ale...@cs...> - 2014-01-31 01:06:32
|
Are they duplicate (two identical proteins) from one contig or two proteins (different coordinates) in a contig? A -- Alexie Papanicolaou CSIRO Ecosystem Sciences ________________________________ From: Zhang, Ning Sent: Thursday, 30 January 2014 9:56:19 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: <tra...@li...> Subject: Re: [Transdecoder-users] problems of installation Hi, all: I found that there are some duplicate peptides in *.transdecoder.pep. What happened? How can I get only one peptide for each contig, maybe the longest one. Thanks Ning On Jan 25, 2014, at 7:55 AM, Zhang, Ning wrote: yes, I made it. After installing this module, it works. If you use Transdecoder on cluster, you had better install the module at your own path. A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help. Ning On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: It seems that you or your sysadmin will have to install the perl module: $ cpan URI::Escape If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle... a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744> -- ResearcherID<https://urldefense.proofpoint.com/v1/url?u=http://www.researcherid.com/rid/A-1618-2011&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=5b2d419ad1f31ad2bbaadeb5d7c6b74bd08888dd929ae8933194347cc2dd0d3e> -- Bioinformatics is also an experimental science ________________________________ From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>] Sent: Saturday, 25 January 2014 6:06 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] problems of installation Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrk&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=d5aa942dbe90f9c4cee4ace02d5ae1325472ee07cfbb022ee55849276e387cdb_______________________________________________ Transdecoder-users mailing list Tra...@li... https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/transdecoder-users&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=8c9eb782b20a3b7360b0edc5a5b5bc9fec97c9de3a1f28a000673bb1f01d8bae |
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From: Zhang, N. <Zh...@si...> - 2014-01-30 21:56:28
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Hi, all: I found that there are some duplicate peptides in *.transdecoder.pep. What happened? How can I get only one peptide for each contig, maybe the longest one. Thanks Ning On Jan 25, 2014, at 7:55 AM, Zhang, Ning wrote: yes, I made it. After installing this module, it works. If you use Transdecoder on cluster, you had better install the module at your own path. A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help. Ning On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: It seems that you or your sysadmin will have to install the perl module: $ cpan URI::Escape If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle... a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744> -- ResearcherID<https://urldefense.proofpoint.com/v1/url?u=http://www.researcherid.com/rid/A-1618-2011&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=5b2d419ad1f31ad2bbaadeb5d7c6b74bd08888dd929ae8933194347cc2dd0d3e> -- Bioinformatics is also an experimental science ________________________________ From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>] Sent: Saturday, 25 January 2014 6:06 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] problems of installation Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrk&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=d5aa942dbe90f9c4cee4ace02d5ae1325472ee07cfbb022ee55849276e387cdb_______________________________________________ Transdecoder-users mailing list Tra...@li... https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/transdecoder-users&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=Y7O%2FsAwF6WOeHlIyNChT%2BwaySpIVL8mcPQA5zguHj4s%3D%0A&s=8c9eb782b20a3b7360b0edc5a5b5bc9fec97c9de3a1f28a000673bb1f01d8bae |
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From: Zhang, N. <Zh...@si...> - 2014-01-25 12:55:44
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yes, I made it. After installing this module, it works. If you use Transdecoder on cluster, you had better install the module at your own path. A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help. Ning On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>> <Ale...@cs...<mailto:Ale...@cs...>> wrote: It seems that you or your sysadmin will have to install the perl module: $ cpan URI::Escape If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle... a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744> -- ResearcherID<https://urldefense.proofpoint.com/v1/url?u=http://www.researcherid.com/rid/A-1618-2011&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=5b2d419ad1f31ad2bbaadeb5d7c6b74bd08888dd929ae8933194347cc2dd0d3e> -- Bioinformatics is also an experimental science ________________________________ From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>] Sent: Saturday, 25 January 2014 6:06 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] problems of installation Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang |
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From: <Ale...@cs...> - 2014-01-25 06:33:23
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It seems that you or your sysadmin will have to install the perl module: $ cpan URI::Escape If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle... a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Zhang, Ning [Zh...@si...] Sent: Saturday, 25 January 2014 6:06 AM To: tra...@li... Subject: [Transdecoder-users] problems of installation Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang |
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From: Zhang, N. <Zh...@si...> - 2014-01-24 19:36:47
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Hi, all: I installed the latest Transdecoder with the command "make", however, when I run it, I got error message. Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15. Compilation failed in require at ./TransDecoder line 102. BEGIN failed--compilation aborted at ./TransDecoder line 102. what is wrong with my installation. Thanks. Ning Zhang |
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From: <Ale...@cs...> - 2014-01-16 10:15:14
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Hello I've reverted the change of FFINDEX being statically linked. It is now dynamic again. If not configured correctly and user wants to user MPI, the software complains and asks you to read the manual. new release uploaded thanks a ________________________________ From: Papanicolaou, Alexie (CES, Black Mountain) Sent: Monday, 13 January 2014 12:26 PM To: Matthew MacManes Cc: tra...@li... Subject: RE: [Transdecoder-users] make fails I assume this is working ok now. I'm making a new release now. p.s the ffindex issues were documented on the website but I guess most people don't read the manual :-) I'll remove the relevant help text as it is now statically linked -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Matthew MacManes [mac...@gm...] Sent: Saturday, 11 January 2014 11:54 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: tra...@li... Subject: Re: [Transdecoder-users] make fails Alexie, There is indeed a documented issue with ‘new’ versions of gcc: https://code.google.com/p/cdhit/issues/detail?id=12 A newer version will work: curl -L https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz > cd-hit-v4.6.1-2012-08-27.tgz Same make instructions. I’m happy to update the Transdecoder makefile if you give me write access. Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs...<mailto:Ale...@cs...> wrote: Thanks ffindex is now static, pls do a svn update. weird on cd-hit. default make should have been with openmp (-fopenmp). can you please try again? if it is still happening... hmmm I have gcc 4.6.3 or 4.4.3 and it is ok. not sure what is going on, maybe someone with more engineering knowledge can help? ubuntu distributes cd-hit in a repo so i wonder what does apt-get build-dep say? is there a dependency missing from your system (i thought it had no dependencies) a ________________________________ From: Matthew MacManes [mac...@gm...<mailto:mac...@gm...>] Sent: Saturday, 11 January 2014 5:18 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] make fails List, With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3 2 things: make test_ffindex fails: (the shared object libffindex.so.0.1 cannot be found) make test_ffindex cd sample_data && ./__runMe_use_pfam_MPI_ffindex.sh -parsing cufflinks output: transcripts.gtf -parsing genome fasta: test.genome.fasta -done parsing genome. // processing 7000000090838467 CMD: /home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat CMD: /home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest transdecoder.tmp.pfam/base_freqs.dat > transdecoder.tmp.pfam/hexamer.scores CMD: /home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.pfam/longest_orfs.cds transdecoder.tmp.pfam/hexamer.scores > transdecoder.tmp.pfam/longest_orfs.cds.scores CMD: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug Partitioning fasta file transdecoder.tmp.pfam/longest_orfs.pep CMD: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory Error, cmd: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at /home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192. Error, cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug died with ret 512 at ../TransDecoder line 493. make: *** [test_ffindex] Error 2 libffindex.so.0.1 is in ffindex/lib64, but this is not in my path, not will it be in most users. make fails on cd-hit: g++ -O2 -DNO_OPENMP cdhit-common.c++ -c cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’: cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat] cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const Options&)’: cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, const Options&)’: cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const Options&)’: cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] In file included from cdhit-common.c++:28:0: cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]’: cdhit-common.c++:704:27: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]’: cdhit-common.c++:705:25: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]’: cdhit-common.c++:1247:24: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’: cdhit-common.c++:1895:26: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, std::allocator<int> >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead make: *** [cdhit-common.o] Error 1 Thanks, Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall |
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From: <Ale...@cs...> - 2014-01-13 01:27:20
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I assume this is working ok now. I'm making a new release now. p.s the ffindex issues were documented on the website but I guess most people don't read the manual :-) I'll remove the relevant help text as it is now statically linked -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Matthew MacManes [mac...@gm...] Sent: Saturday, 11 January 2014 11:54 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: tra...@li... Subject: Re: [Transdecoder-users] make fails Alexie, There is indeed a documented issue with ‘new’ versions of gcc: https://code.google.com/p/cdhit/issues/detail?id=12 A newer version will work: curl -L https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz > cd-hit-v4.6.1-2012-08-27.tgz Same make instructions. I’m happy to update the Transdecoder makefile if you give me write access. Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs...<mailto:Ale...@cs...> wrote: Thanks ffindex is now static, pls do a svn update. weird on cd-hit. default make should have been with openmp (-fopenmp). can you please try again? if it is still happening... hmmm I have gcc 4.6.3 or 4.4.3 and it is ok. not sure what is going on, maybe someone with more engineering knowledge can help? ubuntu distributes cd-hit in a repo so i wonder what does apt-get build-dep say? is there a dependency missing from your system (i thought it had no dependencies) a ________________________________ From: Matthew MacManes [mac...@gm...<mailto:mac...@gm...>] Sent: Saturday, 11 January 2014 5:18 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] make fails List, With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3 2 things: make test_ffindex fails: (the shared object libffindex.so.0.1 cannot be found) make test_ffindex cd sample_data && ./__runMe_use_pfam_MPI_ffindex.sh -parsing cufflinks output: transcripts.gtf -parsing genome fasta: test.genome.fasta -done parsing genome. // processing 7000000090838467 CMD: /home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat CMD: /home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest transdecoder.tmp.pfam/base_freqs.dat > transdecoder.tmp.pfam/hexamer.scores CMD: /home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.pfam/longest_orfs.cds transdecoder.tmp.pfam/hexamer.scores > transdecoder.tmp.pfam/longest_orfs.cds.scores CMD: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug Partitioning fasta file transdecoder.tmp.pfam/longest_orfs.pep CMD: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory Error, cmd: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at /home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192. Error, cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug died with ret 512 at ../TransDecoder line 493. make: *** [test_ffindex] Error 2 libffindex.so.0.1 is in ffindex/lib64, but this is not in my path, not will it be in most users. make fails on cd-hit: g++ -O2 -DNO_OPENMP cdhit-common.c++ -c cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’: cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat] cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const Options&)’: cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, const Options&)’: cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const Options&)’: cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] In file included from cdhit-common.c++:28:0: cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]’: cdhit-common.c++:704:27: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]’: cdhit-common.c++:705:25: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]’: cdhit-common.c++:1247:24: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’: cdhit-common.c++:1895:26: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, std::allocator<int> >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead make: *** [cdhit-common.o] Error 1 Thanks, Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall |
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From: <Ale...@cs...> - 2014-01-11 13:00:08
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thank you. svn committed a ________________________________ From: Matthew MacManes [mac...@gm...] Sent: Saturday, 11 January 2014 11:54 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: tra...@li... Subject: Re: [Transdecoder-users] make fails Alexie, There is indeed a documented issue with ‘new’ versions of gcc: https://code.google.com/p/cdhit/issues/detail?id=12 A newer version will work: curl -L https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz > cd-hit-v4.6.1-2012-08-27.tgz Same make instructions. I’m happy to update the Transdecoder makefile if you give me write access. Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs...<mailto:Ale...@cs...> wrote: Thanks ffindex is now static, pls do a svn update. weird on cd-hit. default make should have been with openmp (-fopenmp). can you please try again? if it is still happening... hmmm I have gcc 4.6.3 or 4.4.3 and it is ok. not sure what is going on, maybe someone with more engineering knowledge can help? ubuntu distributes cd-hit in a repo so i wonder what does apt-get build-dep say? is there a dependency missing from your system (i thought it had no dependencies) a ________________________________ From: Matthew MacManes [mac...@gm...<mailto:mac...@gm...>] Sent: Saturday, 11 January 2014 5:18 AM To: tra...@li...<mailto:tra...@li...> Subject: [Transdecoder-users] make fails List, With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3 2 things: make test_ffindex fails: (the shared object libffindex.so.0.1 cannot be found) make test_ffindex cd sample_data && ./__runMe_use_pfam_MPI_ffindex.sh -parsing cufflinks output: transcripts.gtf -parsing genome fasta: test.genome.fasta -done parsing genome. // processing 7000000090838467 CMD: /home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat CMD: /home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest transdecoder.tmp.pfam/base_freqs.dat > transdecoder.tmp.pfam/hexamer.scores CMD: /home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.pfam/longest_orfs.cds transdecoder.tmp.pfam/hexamer.scores > transdecoder.tmp.pfam/longest_orfs.cds.scores CMD: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug Partitioning fasta file transdecoder.tmp.pfam/longest_orfs.pep CMD: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory Error, cmd: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at /home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192. Error, cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug died with ret 512 at ../TransDecoder line 493. make: *** [test_ffindex] Error 2 libffindex.so.0.1 is in ffindex/lib64, but this is not in my path, not will it be in most users. make fails on cd-hit: g++ -O2 -DNO_OPENMP cdhit-common.c++ -c cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’: cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat] cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const Options&)’: cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, const Options&)’: cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat] cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const Options&)’: cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] In file included from cdhit-common.c++:28:0: cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]’: cdhit-common.c++:704:27: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]’: cdhit-common.c++:705:25: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]’: cdhit-common.c++:1247:24: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’: cdhit-common.c++:1895:26: required from here cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, std::allocator<int> >’ are not found by unqualified lookup cdhit-common.h:95:4: note: use ‘this->push_back’ instead make: *** [cdhit-common.o] Error 1 Thanks, Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall |
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From: Matthew M. <mac...@gm...> - 2014-01-11 12:54:27
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Alexie, There is indeed a documented issue with ‘new’ versions of gcc: https://code.google.com/p/cdhit/issues/detail?id=12 A newer version will work: curl -L https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz > cd-hit-v4.6.1-2012-08-27.tgz Same make instructions. I’m happy to update the Transdecoder makefile if you give me write access. Matt _____________________________________ Matthew MacManes, Ph.D. University of New Hampshire I Assistant Professor Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 I Twitter: @PeroMHC Web: genomebio.org Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs... wrote: > Thanks > ffindex is now static, pls do a svn update. > > weird on cd-hit. default make should have been with openmp (-fopenmp). can you please try again? > > if it is still happening... hmmm I have gcc 4.6.3 or 4.4.3 and it is ok. not sure what is going on, maybe someone with more engineering knowledge can help? ubuntu distributes cd-hit in a repo so i wonder what does apt-get build-dep say? is there a dependency missing from your system (i thought it had no dependencies) > > a > > > From: Matthew MacManes [mac...@gm...] > Sent: Saturday, 11 January 2014 5:18 AM > To: tra...@li... > Subject: [Transdecoder-users] make fails > > List, > > With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3 > > 2 things: > > make test_ffindex fails: (the shared object libffindex.so.0.1 cannot be found) > > make test_ffindex > cd sample_data && ./__runMe_use_pfam_MPI_ffindex.sh > -parsing cufflinks output: transcripts.gtf > -parsing genome fasta: test.genome.fasta > -done parsing genome. > // processing 7000000090838467 > CMD: /home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat > CMD: /home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest transdecoder.tmp.pfam/base_freqs.dat > transdecoder.tmp.pfam/hexamer.scores > CMD: /home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.pfam/longest_orfs.cds transdecoder.tmp.pfam/hexamer.scores > transdecoder.tmp.pfam/longest_orfs.cds.scores > CMD: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug > Partitioning fasta file transdecoder.tmp.pfam/longest_orfs.pep > CMD: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa > /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory > Error, cmd: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at /home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192. > Error, cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug died with ret 512 at ../TransDecoder line 493. > make: *** [test_ffindex] Error 2 > > > libffindex.so.0.1 is in ffindex/lib64, but this is not in my path, not will it be in most users. > > > make fails on cd-hit: > g++ -O2 -DNO_OPENMP cdhit-common.c++ -c > cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’: > cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat] > cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const Options&)’: > cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, const Options&)’: > cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat] > cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] > cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const Options&)’: > cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat] > In file included from cdhit-common.c++:28:0: > cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]’: > cdhit-common.c++:704:27: required from here > cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] > cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are not found by unqualified lookup > cdhit-common.h:95:4: note: use ‘this->push_back’ instead > cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]’: > cdhit-common.c++:705:25: required from here > cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] > cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found by unqualified lookup > cdhit-common.h:95:4: note: use ‘this->push_back’ instead > cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]’: > cdhit-common.c++:1247:24: required from here > cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] > cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by unqualified lookup > cdhit-common.h:95:4: note: use ‘this->push_back’ instead > cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’: > cdhit-common.c++:1895:26: required from here > cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] > cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, std::allocator<int> >’ are not found by unqualified lookup > cdhit-common.h:95:4: note: use ‘this->push_back’ instead > make: *** [cdhit-common.o] Error 1 > > Thanks, Matt > > _____________________________________ > Matthew MacManes, Ph.D. > University of New Hampshire I Assistant Professor > Department of Molecular, Cellular, & Biomedical Sciences > Durham, NH 03824 > Phone: 603-862-4052 I Twitter: @PeroMHC > Web: genomebio.org > Office: 189 Rudman Hall > Laboratory: 145 Rudman Hall > |
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From: <Ale...@cs...> - 2014-01-11 05:25:48
|
Thanks
ffindex is now static, pls do a svn update.
weird on cd-hit. default make should have been with openmp (-fopenmp). can you please try again?
if it is still happening... hmmm I have gcc 4.6.3 or 4.4.3 and it is ok. not sure what is going on, maybe someone with more engineering knowledge can help? ubuntu distributes cd-hit in a repo so i wonder what does apt-get build-dep say? is there a dependency missing from your system (i thought it had no dependencies)
a
________________________________
From: Matthew MacManes [mac...@gm...]
Sent: Saturday, 11 January 2014 5:18 AM
To: tra...@li...
Subject: [Transdecoder-users] make fails
List,
With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3
2 things:
make test_ffindex fails: (the shared object libffindex.so.0.1 cannot be found)
make test_ffindex
cd sample_data && ./__runMe_use_pfam_MPI_ffindex.sh
-parsing cufflinks output: transcripts.gtf
-parsing genome fasta: test.genome.fasta
-done parsing genome.
// processing 7000000090838467
CMD: /home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat
CMD: /home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest transdecoder.tmp.pfam/base_freqs.dat > transdecoder.tmp.pfam/hexamer.scores
CMD: /home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.pfam/longest_orfs.cds transdecoder.tmp.pfam/hexamer.scores > transdecoder.tmp.pfam/longest_orfs.cds.scores
CMD: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug
Partitioning fasta file transdecoder.tmp.pfam/longest_orfs.pep
CMD: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa
/home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory
Error, cmd: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at /home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192.
Error, cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat --MPI --workdir transdecoder.tmp.pfam --debug died with ret 512 at ../TransDecoder line 493.
make: *** [test_ffindex] Error 2
libffindex.so.0.1 is in ffindex/lib64, but this is not in my path, not will it be in most users.
make fails on cd-hit:
g++ -O2 -DNO_OPENMP cdhit-common.c++ -c
cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’:
cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat]
cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const Options&)’:
cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, const Options&)’:
cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const Options&)’:
cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat]
In file included from cdhit-common.c++:28:0:
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]’:
cdhit-common.c++:704:27: required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]’:
cdhit-common.c++:705:25: required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]’:
cdhit-common.c++:1247:24: required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’:
cdhit-common.c++:1895:26: required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, std::allocator<int> >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
make: *** [cdhit-common.o] Error 1
Thanks, Matt
_____________________________________
Matthew MacManes, Ph.D.
University of New Hampshire I Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH 03824
Phone: 603-862-4052 I Twitter: @PeroMHC<https://twitter.com/PeroMHC>
Web: genomebio.org<http://genomebio.org/>
Office: 189 Rudman Hall
Laboratory: 145 Rudman Hall
|
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From: Matthew M. <mac...@gm...> - 2014-01-10 18:18:18
|
<html><head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1"></head><body
style="font-family: Avenir;" text="#000000" bgcolor="#FFFFFF">
<div style="font-family: Avenir;"><span style="font-family: Avenir;">List,
<br><br>With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3<br><br>2
things:<br><br>make test_ffindex fails: (the shared object <span
style="font-weight: bold;">libffindex.so.0.1</span> cannot be found)<br><br>make
test_ffindex<br>cd sample_data &&
./__runMe_use_pfam_MPI_ffindex.sh<br>-parsing cufflinks output:
transcripts.gtf<br>-parsing genome fasta: test.genome.fasta<br>-done
parsing genome.<br>// processing 7000000090838467<br>CMD:
/home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl
transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat<br>CMD:
/home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl
transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest
transdecoder.tmp.pfam/base_freqs.dat >
transdecoder.tmp.pfam/hexamer.scores<br>CMD:
/home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl
transdecoder.tmp.pfam/longest_orfs.cds
transdecoder.tmp.pfam/hexamer.scores >
transdecoder.tmp.pfam/longest_orfs.cds.scores<br>CMD:
/home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep
transdecoder.tmp.pfam/longest_orfs.pep --pfam_db
/media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o
transcripts.fasta.transdecoder.pfam.dat --MPI --workdir
transdecoder.tmp.pfam --debug<br>Partitioning fasta file
transdecoder.tmp.pfam/longest_orfs.pep<br>CMD:
/home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s
transdecoder.tmp.pfam/partition.0.fa.db
transdecoder.tmp.pfam/partition.0.fa.db.idx
transdecoder.tmp.pfam/partition.0.fa<br><span style="text-decoration:
underline; color: rgb(255, 0, 0);">/home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta:
error while loading shared libraries: libffindex.so.0.1: cannot open
shared object file: No such file or directory</span><br>Error, cmd:
/home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s
transdecoder.tmp.pfam/partition.0.fa.db
transdecoder.tmp.pfam/partition.0.fa.db.idx
transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at
/home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192.<br>Error,
cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep
transdecoder.tmp.pfam/longest_orfs.pep --pfam_db
/media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o
transcripts.fasta.transdecoder.pfam.dat --MPI --workdir
transdecoder.tmp.pfam --debug died with ret 512 at ../TransDecoder
line 493.<br>make: *** [test_ffindex] Error 2<br><br><br>libffindex.so.0.1
is in ffindex/lib64, but this is not in my path, not will it be in most
users. <br><br><br><span style="font-weight: bold;">make fails on
cd-hit:</span><br>g++ -O2 -DNO_OPENMP cdhit-common.c++ -c<br>cdhit-common.c++:
In constructor ‘TempFile::TempFile(const char*)’:<br>cdhit-common.c++:68:34:
warning: format ‘%x’ expects argument of type ‘unsigned int’, but
argument 3 has type ‘TempFile*’ [-Wformat]<br>cdhit-common.c++: In
member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const
Options&)’:<br>cdhit-common.c++:2258:47: warning: format ‘%i’
expects argument of type ‘int’, but argument 3 has type ‘size_t {aka
long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2262:71: warning:
format ‘%i’ expects argument of type ‘int’, but argument 4 has type
‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2262:71:
warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2266:78:
warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2266:78:
warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2271:52:
warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2274:51:
warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2279:30:
warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:
In member function ‘void SequenceDB::DoClustering(int, const
Options&)’:<br>cdhit-common.c++:2476:90: warning: format ‘%i’
expects argument of type ‘int’, but argument 2 has type
‘std::vector<Sequence*, std::allocator<Sequence*>
>::size_type {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:2487:65:
warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>cdhit-common.c++:
In member function ‘void SequenceDB::DoClustering(const Options&)’:<br>cdhit-common.c++:2994:65:
warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has
type ‘size_t {aka long unsigned int}’ [-Wformat]<br>In file included
from cdhit-common.c++:28:0:<br>cdhit-common.h: In instantiation of ‘void
Vector<TYPE>::Append(const TYPE&) [with TYPE =
NVector<long int>]’:<br>cdhit-common.c++:704:27: required from
here<br>cdhit-common.h:95:4: error: ‘push_back’ was not declared in this
scope, and no declarations were found by argument-dependent lookup at
the point of instantiation [-fpermissive]<br>cdhit-common.h:95:4: note:
declarations in dependent base ‘std::vector<NVector<long int>,
std::allocator<NVector<long int> > >’ are not found by
unqualified lookup<br>cdhit-common.h:95:4: note: use
‘this->push_back’ instead<br>cdhit-common.h: In instantiation of
‘void Vector<TYPE>::Append(const TYPE&) [with TYPE =
NVector<int>]’:<br>cdhit-common.c++:705:25: required from here<br>cdhit-common.h:95:4:
error: ‘push_back’ was not declared in this scope, and no declarations
were found by argument-dependent lookup at the point of instantiation
[-fpermissive]<br>cdhit-common.h:95:4: note: declarations in dependent
base ‘std::vector<NVector<int>,
std::allocator<NVector<int> > >’ are not found by
unqualified lookup<br>cdhit-common.h:95:4: note: use
‘this->push_back’ instead<br>cdhit-common.h: In instantiation of
‘void Vector<TYPE>::Append(const TYPE&) [with TYPE =
Sequence*]’:<br>cdhit-common.c++:1247:24: required from here<br>cdhit-common.h:95:4:
error: ‘push_back’ was not declared in this scope, and no declarations
were found by argument-dependent lookup at the point of instantiation
[-fpermissive]<br>cdhit-common.h:95:4: note: declarations in dependent
base ‘std::vector<Sequence*, std::allocator<Sequence*> >’
are not found by unqualified lookup<br>cdhit-common.h:95:4: note: use
‘this->push_back’ instead<br>cdhit-common.h: In instantiation of
‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’:<br>cdhit-common.c++:1895:26:
required from here<br>cdhit-common.h:95:4: error: ‘push_back’ was not
declared in this scope, and no declarations were found by
argument-dependent lookup at the point of instantiation [-fpermissive]<br>cdhit-common.h:95:4:
note: declarations in dependent base ‘std::vector<int,
std::allocator<int> >’ are not found by unqualified lookup<br>cdhit-common.h:95:4:
note: use ‘this->push_back’ instead<br>make: *** [cdhit-common.o]
Error 1<br><br></span>Thanks, Matt<br><div class="moz-signature"><br><span
style="font-family: Avenir;">_____________________________________<br>
Matthew MacManes, Ph.D. <br>
University of New Hampshire I Assistant Professor<br>
Department of Molecular, Cellular, & Biomedical Sciences<br>
Durham, NH 03824<br>
Phone: 603-862-4052 I Twitter: <a href="https://twitter.com/PeroMHC">@PeroMHC</a><br>
Web: <a href="http://genomebio.org/">genomebio.org</a><br>
Office: 189 Rudman Hall<br>
Laboratory: 145 Rudman Hall<br>
<br>
</span></div></div>
</body>
</html>
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From: Jahn D. <jah...@bi...> - 2013-12-27 07:48:35
|
Dr Papanicolaou, That did not work on my machine. So after the gunzip -c Pf*gz > Pfam-AB.hmm I did, hmmpress Pfam-AB.hmm and proceeded to the 'hmmscan' call. Should be OK? Not? Jahn xxxxxxxxxxxxxxxxxx Dr Jahn Davik Bioforsk Kvithamar N-7512 Stjordal Norway cell: (+47) 979 54 473 switch: +47 4060 4100 sentralbord: 03246 skype: jahn.davik Fra: Ale...@cs... [mailto:Ale...@cs...] Sendt: 21. desember 2013 03:18 Til: bh...@br...; tra...@li... Emne: Re: [Transdecoder-users] response to Kate Hello It was downloaded the same day as the files were uploaded (17th of November 2013). You can download the latest one ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ Pfam-A.hmm.gz Pfam-B.hmm.gz concatanate them and create a new binary version gunzip -c Pf*gz > Pfam-AB.hmm hmmconvert -b Pfam-AB.hmm > Pfam-AB.hmm.bin place Pfam-AB.hmm.bin in /pfam (deleting any existing files) and run make prep_pfam i'll update the instructions for the next release a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Brian Haas [bh...@br...] Sent: Saturday, 21 December 2013 9:10 AM To: tra...@li...<mailto:tra...@li...> Cc: Papanicolaou, Alexie (CES, Black Mountain) Subject: response to Kate Hi Kate, Alexie (CC'd) will be able to tell you for sure how old the provided version of pfam-AB is. I suspect it was from earlier this year. You might want to just pull down the very latest version of the database, though, from the pfam website. best, ~brian Hi, I am just wondering how old the provided Pfam AB database is? Using Transdecoder +/- PFAM search with the provided AB dataset, I get very few additional hits being included. If you don't think that getting the VERY newest version should affect results greatly, I won't worry about it. My organism is very non-model... P. falciparum malaria, so maybe PFAM searching just isn't so great for my organism? Also, am I correct that the minimum length cutoff is in effect no matter what? I.e something with a PFAM score above noise but shorter than length cutoff won't make the final list. Thanks! And happiest holidays :) Kate -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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From: <Ale...@cs...> - 2013-12-21 02:34:12
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I'ts not really minimum length but an added option to keep long putative ORFs without any evidence for coding potential If a protein is larger than the --retain_long_orfs, it will be reported regardless of lack of evidence (PFAM, hexamer score etc). Anything with a PFAM score or other evidence but shorter than --retain_long_orfs, will be reported. I've updated the USAGE help for the next release thanks a ________________________________ From: Brian Haas [bh...@br...] Sent: Saturday, 21 December 2013 9:10 AM To: tra...@li... Cc: Papanicolaou, Alexie (CES, Black Mountain) Subject: response to Kate Hi Kate, Alexie (CC'd) will be able to tell you for sure how old the provided version of pfam-AB is. I suspect it was from earlier this year. You might want to just pull down the very latest version of the database, though, from the pfam website. best, ~brian Hi, I am just wondering how old the provided Pfam AB database is? Using Transdecoder +/- PFAM search with the provided AB dataset, I get very few additional hits being included. If you don't think that getting the VERY newest version should affect results greatly, I won't worry about it. My organism is very non-model... P. falciparum malaria, so maybe PFAM searching just isn't so great for my organism? Also, am I correct that the minimum length cutoff is in effect no matter what? I.e something with a PFAM score above noise but shorter than length cutoff won't make the final list. Thanks! And happiest holidays :) Kate -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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From: <Ale...@cs...> - 2013-12-21 02:30:22
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Hello It was downloaded the same day as the files were uploaded (17th of November 2013). You can download the latest one ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ Pfam-A.hmm.gz Pfam-B.hmm.gz concatanate them and create a new binary version gunzip -c Pf*gz > Pfam-AB.hmm hmmconvert -b Pfam-AB.hmm > Pfam-AB.hmm.bin place Pfam-AB.hmm.bin in /pfam (deleting any existing files) and run make prep_pfam i'll update the instructions for the next release a -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Brian Haas [bh...@br...] Sent: Saturday, 21 December 2013 9:10 AM To: tra...@li... Cc: Papanicolaou, Alexie (CES, Black Mountain) Subject: response to Kate Hi Kate, Alexie (CC'd) will be able to tell you for sure how old the provided version of pfam-AB is. I suspect it was from earlier this year. You might want to just pull down the very latest version of the database, though, from the pfam website. best, ~brian Hi, I am just wondering how old the provided Pfam AB database is? Using Transdecoder +/- PFAM search with the provided AB dataset, I get very few additional hits being included. If you don't think that getting the VERY newest version should affect results greatly, I won't worry about it. My organism is very non-model... P. falciparum malaria, so maybe PFAM searching just isn't so great for my organism? Also, am I correct that the minimum length cutoff is in effect no matter what? I.e something with a PFAM score above noise but shorter than length cutoff won't make the final list. Thanks! And happiest holidays :) Kate -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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From: Brian H. <bh...@br...> - 2013-12-20 22:10:31
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Hi Kate, Alexie (CC'd) will be able to tell you for sure how old the provided version of pfam-AB is. I suspect it was from earlier this year. You might want to just pull down the very latest version of the database, though, from the pfam website. best, ~brian Hi, I am just wondering how old the provided Pfam AB database is? Using Transdecoder +/- PFAM search with the provided AB dataset, I get very few additional hits being included. If you don't think that getting the VERY newest version should affect results greatly, I won't worry about it. My organism is very non-model... P. falciparum malaria, so maybe PFAM searching just isn't so great for my organism? Also, am I correct that the minimum length cutoff is in effect no matter what? I.e something with a PFAM score above noise but shorter than length cutoff won't make the final list. Thanks! And happiest holidays :) Kate -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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