Question: error will using transdecoder.predict
0
gravatar for najibveto
2.8 years ago by
najibveto40
Korea, Republic Of
najibveto40 wrote:

hello i am using transdecoder to get the longest orf after that i blasted them against zebrafish proteins database and while i wanted to integrate the blast results i got this error:

najib@najib-VirtualBox:~/Downloads/TransDecoder-3.0.1$ perl TransDecoder.Predict -t fatheadminnow.fasta --retain_blastp_hits blastp.outfmt6

#####################
Counts of kept entries according to attributes:
BLASTP|FRAMESCORE|LONGORF   22069
BLASTP|FRAMESCORE   15283
FRAMESCORE  3298
BLASTP  946
LONGORF 444
FRAMESCORE|LONGORF  321
BLASTP|LONGORF  149
########################

Command:

/home/najib/Downloads/TransDecoder-3.0.1/util/index_gff3_files_by_isoform.pl fatheadminnow.fasta.transdecoder_dir/longest_orfs.gff3
Can't load '/home/najib/miniconda3/lib/perl5/5.22.0/x86_64-linux-thread-multi/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/najib/miniconda3/lib/perl5/5.22.0/XSLoader.pm line 70.
 at /home/najib/miniconda3/lib/perl5/5.22.0/x86_64-linux-thread-multi/DB_File.pm line 255.
Compilation failed in require at /home/najib/Downloads/TransDecoder-3.0.1/util/../PerlLib/TiedHash.pm line 6.
BEGIN failed--compilation aborted at /home/najib/Downloads/TransDecoder-3.0.1/util/../PerlLib/TiedHash.pm line 6.
Compilation failed in require at /home/najib/miniconda3/lib/perl5/5.22.0/base.pm line 99.
    ...propagated at /home/najib/miniconda3/lib/perl5/5.22.0/base.pm line 108.
BEGIN failed--compilation aborted at /home/najib/Downloads/TransDecoder-3.0.1/util/../PerlLib/Gene_obj_indexer.pm line 6.
Compilation failed in require at /home/najib/Downloads/TransDecoder-3.0.1/util/index_gff3_files_by_isoform.pl line 8.
BEGIN failed--compilation aborted at /home/najib/Downloads/TransDecoder-3.0.1/util/index_gff3_files_by_isoform.pl line 8.
Error, cmd: /home/najib/Downloads/TransDecoder-3.0.1/util/index_gff3_files_by_isoform.pl fatheadminnow.fasta.transdecoder_dir/longest_orfs.gff3 died with ret 512 at TransDecoder.Predict line 379.
najib@najib-VirtualBox:~/Downloads/TransDecoder-3.0.1$

can someone tell me what is missing and what is the solution for it? thanks for your help.

transcriptome transdecoder • 1.2k views
ADD COMMENTlink modified 2.8 years ago by EVR560 • written 2.8 years ago by najibveto40
0
gravatar for EVR
2.8 years ago by
EVR560
Earth
EVR560 wrote:

Hi,

Kindly check whether yyou have installed all the rpel mdules required by Transdecoder. It seems that library "XSLoader.pm " is totlally missing. Kindly re install and re-run the programm

ADD COMMENTlink written 2.8 years ago by EVR560
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