DB_File module error

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Olukayode Daramola

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May 11, 2018, 8:20:26 AM5/11/18
to TransDecoder-users
I tried running 

Enter code here./TransDecoder.Predict -t ~/10x_braker/erins_updated10x/braker/Fasciola_hepatica/transcripts.fa...

but I had these errors,

* Running CMD: /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/select_best_ORFs_per_transcript.pl --gff3_file transcripts.fa.transdecoder_dir/longest_orfs.gff3 --cds_scores transcripts.fa.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 749  > transcripts.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3
Selecting best orfsCan't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/../PerlLib /usr/local/share/vcftools_0.1.13/lib/perl5/site_perl/ /usr/local/share/vcftools_0.1.9/lib/perl5/site_perl/ /usr/local/share/MitoSeek-1.3/ /usr/local/share/OLB-1.9.4/lib/perl/ /usr/local/share/PfamScan /usr/local/share/CEGMA_v2.5//lib /usr/local/share/ensembl-api/ensembl/modules /usr/local/share/ensembl-api/ensembl-variation/modules /usr/local/share/ensembl-api/ensembl-compara/modules /usr/local/share/ensembl-api/ensembl-functgenomics/modules /usr/local/share/circos-0.69-5/lib /usr/local/share/sanger-pathogens-Roary-459fd8e/lib/ /pub38/kayussky/anaconda3/lib/site_perl/5.26.0/x86_64-linux-thread-multi /pub38/kayussky/anaconda3/lib/site_perl/5.26.0 /pub38/kayussky/anaconda3/lib/5.26.0/x86_64-linux-thread-multi /pub38/kayussky/anaconda3/lib/5.26.0 .) at /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/../PerlLib/TiedHash.pm line 6.
BEGIN failed--compilation aborted at /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/../PerlLib/TiedHash.pm line 6.
Compilation failed in require at /pub38/kayussky/anaconda3/lib/site_perl/5.26.0/base.pm line 100.
        ...propagated at /pub38/kayussky/anaconda3/lib/site_perl/5.26.0/base.pm line 109.
BEGIN failed--compilation aborted at /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/../PerlLib/Gene_obj_indexer.pm line 6.
Compilation failed in require at /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/select_best_ORFs_per_transcript.pl line 8.
BEGIN failed--compilation aborted at /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/select_best_ORFs_per_transcript.pl line 8.
Error, cmd: /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/util/select_best_ORFs_per_transcript.pl --gff3_file transcripts.fa.transdecoder_dir/longest_orfs.gff3 --cds_scores transcripts.fa.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 749  > transcripts.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3  died with ret 512 No such file or directory at /pub38/kayussky/Software/TransDecoder.wiki/TransDecoder-TransDecoder-v5.2.0/PerlLib/Pipeliner.pm line 185.
        Pipeliner::run(Pipeliner=HASH(0x5570c1a416b8)) called at ./TransDecoder.Predict line 371

I attempted installing DB_file;
running make command says:

"/pub38/kayussky/anaconda3/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- DB_File.bs blib/arch/auto/DB_File/DB_File.bs 644
/pub38/kayussky/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -c  -I/usr/local/BerkeleyDB/include -D_REENTRANT -D_GNU_SOURCE --sysroot=/pub38/kayussky/anaconda3/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2   -DVERSION=\"1.841\" -DXS_VERSION=\"1.841\" -fPIC --sysroot=/pub38/kayussky/anaconda3/x86_64-conda_cos6-linux-gnu/sysroot "-I/pub38/kayussky/anaconda3/lib/5.26.0/x86_64-linux-thread-multi/CORE"  -D_NOT_CORE  -DmDB_Prefix_t=size_t -DmDB_Hash_t=u_int32_t   version.c
version.c:30:10: fatal error: db.h: No such file or directory
 #include <db.h>
          ^~~~~~
compilation terminated.
make: *** [version.o] Error 1

Imstalling a lower version of DB_file gives a similar error.


Any Ideas?

Thanks 

Kay

Brian Haas

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May 11, 2018, 8:54:45 AM5/11/18
to Olukayode Daramola, TransDecoder-users
I'll take some time this morning to remove the DB_File requirement.  Stay tuned...

~brian

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Brian Haas

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May 11, 2018, 10:25:28 AM5/11/18
to Olukayode Daramola, TransDecoder-users
I just put out a new release that doesn't have the DB_File requirement:


I hope this works for you,

~brian


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taua...@gmail.com

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Dec 21, 2018, 11:24:27 AM12/21/18
to TransDecoder-users
Dear Brian,

I am running Transdecoder 3.0.0 and I am having the same issue where the program fails not finding the DB_File.pm

I know the new versions don't need it, but these are just a few samples that I would like to keep compatible/same version as I used for all others months ago.
Can I solve it without updating?
My error is:

Can't locate DB_File.pm in @INC (@INC contains: /n/sw/helmod/apps/centos7/Core/TransDecoder/3.0.0-fasrc01/util/../PerlLib /usr/local/lib64/perl5 /usr/local/sh

BEGIN failed--compilation aborted at /n/sw/helmod/apps/centos7/Core/TransDecoder/3.0.0-fasrc01/util/../PerlLib/TiedHash.pm line 6.

Compilation failed in require at (eval 2) line 2.

        ...propagated at /usr/share/perl5/base.pm line 84.

BEGIN failed--compilation aborted at /n/sw/helmod/apps/centos7/Core/TransDecoder/3.0.0-fasrc01/util/../PerlLib/Gene_obj_indexer.pm line 6.

Compilation failed in require at /n/sw/helmod/apps/centos7/Core/TransDecoder/3.0.0-fasrc01/util/index_gff3_files_by_isoform.pl line 8.

BEGIN failed--compilation aborted at /n/sw/helmod/apps/centos7/Core/TransDecoder/3.0.0-fasrc01/util/index_gff3_files_by_isoform.pl line 8.

Error, cmd: /n/sw/helmod/apps/centos7/Core/TransDecoder/3.0.0-fasrc01/util/index_gff3_files_by_isoform.pl Bothropoma_pilula_386247.Unique.fasta.transdecoder_d

~


Thank you very much!
Cheers,
Tauana
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Brian Haas

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Dec 21, 2018, 2:23:19 PM12/21/18
to Tauana Junqueira da Cunha, TransDecoder-users
Hi,

It'd be easiest to go ahead and install the missing module if possible.  You could hack the code to avoid using it, but it's a bit of work.

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taua...@gmail.com

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Dec 21, 2018, 3:07:05 PM12/21/18
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Hi Brian,
What do you mean by install the missing module? I mean, install Transdecoder all again to version 5.4 or is there something I can install to make version 3.0 work?

Thanks!
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Brian Haas

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Dec 21, 2018, 3:10:55 PM12/21/18
to Tauana Junqueira da Cunha, TransDecoder-users
The DB_File is a fairly standard perl module:

and you can install it using standard methods.    If it gives you trouble, just let me know what the errors are.

best,

~b

taua...@gmail.com

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Dec 26, 2018, 6:28:53 PM12/26/18
to TransDecoder-users
Got it Brian, Transdecoder ran normally now. Thanks a lot!
Happy new year! =)

Brian Haas

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Dec 26, 2018, 6:49:34 PM12/26/18
to Tauana Junqueira da Cunha, TransDecoder-users
fantastic!   best of luck!

~b

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