error will using transdecoder.predict
1
0
Entering edit mode
4.9 years ago
najibveto ▴ 60

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 • 2.0k views
ADD COMMENT
0
Entering edit mode
4.9 years ago
EVR ▴ 570

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 COMMENT

Login before adding your answer.

Traffic: 2473 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6