transdecoder-users — Technical support and project announcements

[Transdecoder-users] response to Nicolas Devos

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

Hi Nicolas,

Sorry for the delay...

The system apparently requires the perl module DB_File.  You can get it
here:

http://search.cpan.org/~pmqs/DB_File-1.831/DB_File.pm

or possibly install it via CPAN like so:

     perl -MCPAN -e shell

      install DB_File

though, it'll likely require admin privileges.

best,

~brian




Hi,

I am sorry to bother you all with this but I have been trying to run
TransDecoder without success so far. I believe the installation worked
(including Hmmer and MPI)  but when I try to run TransDecoder the
program dies very quickly and I can't figure out why.  I have pasted
below the log.  It seems like there is maybe an issue with the PATH to
some file but I am not sure how to fix that.
Has anybody seen this error before?

Thanks

Best regards

Nicolas Devos


./TransDecoder -t /home/shawlab/nd28/cribrosum/fullsetofgenes.fasta
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/get_top_longest_fasta_entries.pl
transdecoder.tmp.12401/longest_orfs.cds 2000 >
transdecoder.tmp.12401/redundant_top
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/bin/cd-hit-est
-r 1 -i transdecoder.tmp.12401/redundant_top -o
transdecoder.tmp.12401/redundant_top.nr90 -M 0 -T 2 >/dev/null
2>/dev/null
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/get_top_longest_fasta_entries.pl
transdecoder.tmp.12401/redundant_top.nr90 500 >
transdecoder.tmp.12401/longest_orfs.cds.top_500_longest
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/compute_base_probs.pl
/home/shawlab/nd28/cribrosum/fullsetofgenes.fasta 0 >
transdecoder.tmp.12401/base_freqs.dat
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl
transdecoder.tmp.12401/longest_orfs.cds.top_500_longest
transdecoder.tmp.12401/base_freqs.dat >
transdecoder.tmp.12401/hexamer.scores
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl
transdecoder.tmp.12401/longest_orfs.cds
transdecoder.tmp.12401/hexamer.scores >
transdecoder.tmp.12401/longest_orfs.cds.scores
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl
transdecoder.tmp.12401/longest_orfs.gff3
Can't locate DB_File.pm in @INC (@INC contains:
/home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib
/opt/apps/perl-5.16.2/lib/site_perl/5.16.2/x86_64-linux
/opt/apps/perl-5.16.2/lib/site_perl/5.16.2
/opt/apps/perl-5.16.2/lib/5.16.2/x86_64-linux
/opt/apps/perl-5.16.2/lib/5.16.2 .) at
/home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib/TiedHash.pm
line 6.
BEGIN failed--compilation aborted at
/home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib/TiedHash.pm
line 6.
Compilation failed in require at (eval 2) line 2.
	...propagated at /opt/apps/perl-5.16.2/lib/5.16.2/base.pm line 84.
BEGIN failed--compilation aborted at
/home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib/Gene_obj_indexer.pm
line 6.
Compilation failed in require at
/home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl
line 8.
BEGIN failed--compilation aborted at
/home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl
line 8.
Error, cmd: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl
transdecoder.tmp.12401/longest_orfs.gff3 died with ret 512 at
./TransDecoder line 493.



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

[Transdecoder-users] Transdecoder mailing list

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

Hi all,

Apologies to those that have written to the
Tra...@li...with questions that haven't been
responded to.  There were some technical
difficulties around properly getting this email list set up.

We'll be better attending to this list here-out.

best,

~brian


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

[Transdecoder-users] Pfam AB version

[Kate B. <sk...@gm...>]

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

[Transdecoder-users] TransDecoder failed--compilation aborted

[Nicolas D. <nd...@du...>]

Hi, 

I am sorry to bother you all with this but I have been trying to run TransDecoder without success so far. I believe the installation worked (including Hmmer and MPI)  but when I try to run TransDecoder the program dies very quickly and I can't figure out why.  I have pasted below the log.  It seems like there is maybe an issue with the PATH to some file but I am not sure how to fix that.  
Has anybody seen this error before? 

Thanks 

Best regards

Nicolas Devos 


./TransDecoder -t /home/shawlab/nd28/cribrosum/fullsetofgenes.fasta 
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/get_top_longest_fasta_entries.pl transdecoder.tmp.12401/longest_orfs.cds 2000 > transdecoder.tmp.12401/redundant_top
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/bin/cd-hit-est -r 1 -i transdecoder.tmp.12401/redundant_top -o transdecoder.tmp.12401/redundant_top.nr90 -M 0 -T 2 >/dev/null 2>/dev/null
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/get_top_longest_fasta_entries.pl transdecoder.tmp.12401/redundant_top.nr90 500 > transdecoder.tmp.12401/longest_orfs.cds.top_500_longest
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/compute_base_probs.pl /home/shawlab/nd28/cribrosum/fullsetofgenes.fasta 0 > transdecoder.tmp.12401/base_freqs.dat
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.12401/longest_orfs.cds.top_500_longest transdecoder.tmp.12401/base_freqs.dat > transdecoder.tmp.12401/hexamer.scores
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.12401/longest_orfs.cds transdecoder.tmp.12401/hexamer.scores > transdecoder.tmp.12401/longest_orfs.cds.scores
CMD: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl transdecoder.tmp.12401/longest_orfs.gff3
Can't locate DB_File.pm in @INC (@INC contains: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib /opt/apps/perl-5.16.2/lib/site_perl/5.16.2/x86_64-linux /opt/apps/perl-5.16.2/lib/site_perl/5.16.2 /opt/apps/perl-5.16.2/lib/5.16.2/x86_64-linux /opt/apps/perl-5.16.2/lib/5.16.2 .) at /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib/TiedHash.pm line 6.
BEGIN failed--compilation aborted at /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib/TiedHash.pm line 6.
Compilation failed in require at (eval 2) line 2.
	...propagated at /opt/apps/perl-5.16.2/lib/5.16.2/base.pm line 84.
BEGIN failed--compilation aborted at /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/../PerlLib/Gene_obj_indexer.pm line 6.
Compilation failed in require at /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl line 8.
BEGIN failed--compilation aborted at /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl line 8.
Error, cmd: /home/shawlab/nd28/bin/executables/TransDecoder_r20131117/util/index_gff3_files_by_isoform.pl transdecoder.tmp.12401/longest_orfs.gff3 died with ret 512 at ./TransDecoder line 493.