[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.