problem even with dbi installed, error DB_file

[drelo]

Sorry to bother you again, I keep getting this error even when I installed db with conda with this line

conda install -c bioconda perl-dbi but when I run it again I got the same error.

I am using perl installed under conda too as seen below.

Thanks for your help!

TransDecoder.Predict -t olivacea_LV034_95.fa  --retain_blastp_hits ./olivacea_LV034_95.fa.transdecoder_dir/blastp.outfmt6
-- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/get_top_longest_fasta_entries.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds 5000 5000 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000, checkpoint exists.
-- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/exclude_similar_proteins.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr, checkpoint exists.
-- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/get_top_longest_fasta_entries.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_500_longest, checkpoint exists.
PCT_GC: 48.6
-- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/seq_n_baseprobs_to_loglikelihood_vals.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_500_longest olivacea_LV034_95.fa.transdecoder_dir/base_freqs.dat > olivacea_LV034_95.fa.transdecoder_dir/hexamer.scores, checkpoint exists.
-- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/score_CDS_likelihood_all_6_frames.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds olivacea_LV034_95.fa.transdecoder_dir/hexamer.scores > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.scores, checkpoint exists.
* Running CMD: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/select_best_ORFs_per_transcript.pl --gff3_file olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.gff3 --cds_scores olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 749  --blast_hits ./olivacea_LV034_95.fa.transdecoder_dir/blastp.outfmt6  > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 
Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/../PerlLib /home/guillermo/miniconda2/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /home/guillermo/miniconda2/lib/perl5/site_perl/5.22.0 /home/guillermo/miniconda2/lib/perl5/5.22.0/x86_64-linux-thread-multi /home/guillermo/miniconda2/lib/perl5/5.22.0 .) at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/../PerlLib/TiedHash.pm line 6.
BEGIN failed--compilation aborted at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/../PerlLib/TiedHash.pm line 6.
Compilation failed in require at /home/guillermo/miniconda2/lib/perl5/5.22.0/base.pm line 99.
    ...propagated at /home/guillermo/miniconda2/lib/perl5/5.22.0/base.pm line 108.
BEGIN failed--compilation aborted at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/../PerlLib/Gene_obj_indexer.pm line 6.
Compilation failed in require at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/select_best_ORFs_per_transcript.pl line 8.
BEGIN failed--compilation aborted at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/select_best_ORFs_per_transcript.pl line 8.
Error, cmd: /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/util/select_best_ORFs_per_transcript.pl --gff3_file olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.gff3 --cds_scores olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.scores  --min_length_auto_accept 749  --blast_hits ./olivacea_LV034_95.fa.transdecoder_dir/blastp.outfmt6  > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3  died with ret 512 at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/PerlLib/Pipeliner.pm line 166.
    Pipeliner::run(Pipeliner=HASH(0x2ca8738)) called at /home/guillermo/workspace/tesis/6.transdecoder/TransDecoder-TransDecoder-v5.0.2/TransDecoder.Predict line 303

[brianjohnhaas]

Hi,

If you're able to directly install the perl module DB_File, this should hopefully work

http://search.cpan.org/~pmqs/DB_File-1.840/DB_File.pm

I don't support the bioconda module so can't help there... Worst case, try downloading it and installing it all outside of bioconda.

best of luck,

~b

On Fri, Mar 16, 2018 at 2:58 PM, Andres Parada notifications@github.com wrote:

Sorry to bother you again, I keep getting this error even when I installed db with conda with this line

conda install -c bioconda perl-dbi but when I run it again I got the same error.

I am using perl installed under conda too as seen below.

Thanks for your help!

`TransDecoder.Predict -t olivacea_LV034_95.fa --retain_blastp_hits ./olivacea_LV034_95.fa.transdecoder_dir/blastp.outfmt6 -- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/get_top_longest_fasta_entries.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds 5000 5000 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000, checkpoint exists. -- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/exclude_similar_proteins.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr, checkpoint exists. -- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/get_top_longest_fasta_entries.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_500_longest, checkpoint exists. PCT_GC: 48.6 -- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/seq_n_baseprobsto loglikelihood_vals.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.top_500_longest olivacea_LV034_95.fa.transdecoder_dir/base_freqs.dat > olivacea_LV034_95.fa.transdecoder_dir/hexamer.scores, checkpoint exists. -- Skipping CMD: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/score_CDS_likelihood_all_6_frames.pl olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds olivacea_LV034_95.fa.transdecoder_dir/hexamer.scores > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.scores, checkpoint exists.

• Running CMD: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/select_best_ORFsper transcript.pl --gff3_file olivacea_LV034_95.fa. transdecoder_dir/longest_orfs.gff3 --cds_scores olivacea_LV034_95.fa. transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 --blast_hits ./olivacea_LV034_95.fa.transdecoder_dir/blastp.outfmt6 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs. cds.best_candidates.gff3 Can't locate DB_File.pm in @inc https://github.com/inc (you may need to install the DB_File module) (@inc https://github.com/inc contains: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/../PerlLib /home/guillermo/miniconda2/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /home/guillermo/miniconda2/lib/perl5/site_perl/5.22.0 /home/guillermo/miniconda2/lib/perl5/5.22.0/x86_64-linux-thread-multi /home/guillermo/miniconda2/lib/perl5/5.22.0 .) at /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/../PerlLib/TiedHash.pm line 6. BEGIN failed--compilation aborted at /home/guillermo/workspace/ tesis/6.transdecoder/TransDecoder-TransDecoder-v5. 0.2/util/../PerlLib/TiedHash.pm line 6. Compilation failed in require at /home/guillermo/miniconda2/ lib/perl5/5.22.0/base.pm line 99. ...propagated at /home/guillermo/miniconda2/lib/perl5/5.22.0/base.pm line 108. BEGIN failed--compilation aborted at /home/guillermo/workspace/ tesis/6.transdecoder/TransDecoder-TransDecoder-v5. 0.2/util/../PerlLib/Gene_obj_indexer.pm line 6. Compilation failed in require at /home/guillermo/workspace/ tesis/6.transdecoder/TransDecoder-TransDecoder-v5. 0.2/util/select_best_ORFs_per_transcript.pl line 8. BEGIN failed--compilation aborted at /home/guillermo/workspace/ tesis/6.transdecoder/TransDecoder-TransDecoder-v5. 0.2/util/select_best_ORFs_per_transcript.pl line 8. Error, cmd: /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/util/select_best_ORFsper transcript.pl --gff3_file olivacea_LV034_95.fa. transdecoder_dir/longest_orfs.gff3 --cds_scores olivacea_LV034_95.fa. transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 --blast_hits ./olivacea_LV034_95.fa.transdecoder_dir/blastp.outfmt6 > olivacea_LV034_95.fa.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 died with ret 512 at /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/PerlLib/Pipeliner.pm line 166. Pipeliner::run(Pipeliner=HASH(0x2ca8738)) called at /home/guillermo/workspace/tesis/6.transdecoder/ TransDecoder-TransDecoder-v5.0.2/TransDecoder.Predict line 303 `

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--

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

[drelo]

**I solved through this line

conda install -c anaconda db4-cos6-x86_64

This adds the db_file associated with the Berkeley DB.**

Thanks!

[drelo]

@brianjohnhaas In case someone else has the same issue, I solved it under conda.

[brianjohnhaas]

great! If you have any additional instructions for anyone, feel free to post. Others use this as a resource.

best,

~b

On Mon, Mar 19, 2018 at 12:06 PM, Andres Parada notifications@github.com wrote:

@brianjohnhaas https://github.com/brianjohnhaas In case someone else has the same issue, I solved it under conda.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/TransDecoder/TransDecoder/issues/58#issuecomment-374266992, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX3LFsINbnNilQXpvHC9oZ91KkOLNks5tf9dtgaJpZM4SuSR_ .

--

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

[drelo]

[I had edited the post above with the correct code, sorry for the confusion] here is the code

first

conda install -c bioconda perl-dbi

I solved de DB_file issue with

conda install -c anaconda db4-cos6-x86_64

I just noticed there is also this option too

conda install -c bioconda perl-db-file

[brianjohnhaas]

Terrific! many thanks for sharing

~b

On Mon, Mar 19, 2018 at 1:28 PM, Andres Parada notifications@github.com wrote:

[I had edited the post above with the correct code, sorry for the confusion] here is the code

first

conda install -c bioconda perl-dbi

I solved de DB_file issue with

conda install -c anaconda db4-cos6-x86_64

[I just noticed there is also this option too conda install -c bioconda perl-db-file ]

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/TransDecoder/TransDecoder/issues/58#issuecomment-374297455, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVXwyk8CzFfA3EMCjt7BOxuesezNh4ks5tf-q3gaJpZM4SuSR_ .

--

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