Re: [Transdecoder-users] Transdecoder running error

[Brian H. <bh...@br...>]

Hi Scott,

To run it and have it run pfam as part of the process, you would run:

TransDecoder -t $your_transcripts.fasta --workdir $your_output_dir_name
--search_pfam $transdecoder_root/pfam/Pfam-AB.hmm.bin

The pfam search is executed after the ORFs have been extracted, and those
ORFs with pfam hits are retained as part of the final set of predictions.

best,

~brian





On Wed, Feb 26, 2014 at 3:25 PM, Geib, Scott <Sco...@ar...>wrote:

>  Hmm, the svn and sample data don't work on the system I was working on,
> but work on another workstation.  Must be something with system
> configuration on my end (maybe NFS?).
>
>
>
> Anyway, not your problem.
>
> Also I was confused a bit on how to run PFAM searches separately, outside
> of Transdecoder.
>
>
> Is this correct:
>
>
>
> ../transdecoder_rel16JAN2014/TransDecoder -t Trinity.fasta -S
> --prepare_pfam
>
> Then I would want to run hmmscan on the longest_orf.pep file.
>
>
>
> Then what is the command to rerun Transdecoder and use the Pfam output?
> The first command seemed to run Transdecoder all the way through without
> using PFAM (not stopping after creation of intermediate files for
> searching).
>
> Just run this from same folder:
>
> ../transdecoder_rel16JAN2014/TransDecoder -t Trinity.fasta -S --pfam_out
> domtbl.out
>
>
>
>
>
>
>
>
>
> *From:* Brian Haas [mailto:bh...@br...]
> *Sent:* Tuesday, February 25, 2014 4:24 AM
> *To:* Geib, Scott
> *Cc:* tra...@li...
> *Subject:* Re: [Transdecoder-users] Transdecoder running error
>
>
>
> Hi Scott,
>
>
>
> It's not obvious what's going on here...   Did the build of the software
> go fine?  (typing 'make' in the base installation directory)
>
>
>
> Is ParaFly working?  You should find it in the distro at:
>
>
>
>   util/bin/ParaFly
>
>
>
> Just try executing it and see if it reports the usage menu.
>
>
>
> For testing, you can go into the provided sample_data/ directory, and
> there are various run-scripts to test different configurations.  I just ran
> the tests in our latest SVN code and it all seems to be working correctly
> (on linux).
>
>
>
> If you want to try the latest SVN code, you can pull it like so:
>
>
>
> svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunktransdecoder-code-0
>
>
>
> best,
>
>
>
> ~brian
>
>
>
>
>
> On Mon, Feb 24, 2014 at 8:58 PM, Geib, Scott <Sco...@ar...>
> wrote:
>
>  I am getting error with Transdecoder and PFAM searching.  Running with
> transdecoder_rel16JAN2014
>
> First if I run hmmscan within TD, I get the following symbolic link error
> (this is stderr):
>
>
>
> CMD:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/util/
> get_top_longest_fasta_entries.pl transdecoder.tmp.9643/longest_orfs.cds
> 2000 > transdecoder.tmp.9643/redundant_top
>
> CMD: /data0/opt/Clustering/cd-hit-v4.5.4-2011-03-07/cd-hit-est -r 1 -i
> transdecoder.tmp.9643/redundant_top -o
> transdecoder.tmp.9643/redundant_top.nr90 -M 0 -T 48 >/dev/null 2>/dev/null
>
> CMD:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/util/
> get_top_longest_fasta_entries.pl transdecoder.tmp.9643/redundant_top.nr90
> 500 > transdecoder.tmp.9643/longest_orfs.cds.top_500_longest
>
> CMD:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/util/
> compute_base_probs.pl Trinity.fasta 1 >
> transdecoder.tmp.9643/base_freqs.dat
>
> CMD:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/util/
> seq_n_baseprobs_to_logliklihood_vals.pltransdecoder.tmp.9643/longest_orfs.cds.top_500_longest
> transdecoder.tmp.9643/base_freqs.dat > transdecoder.tmp.9643/hexamer.scores
>
> CMD:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/util/score_CDS_liklihood_all_6_frames.pl
> transdecoder.tmp.9643/longest_orfs.cds transdecoder.tmp.9643/hexamer.scores
> > transdecoder.tmp.9643/longest_orfs.cds.scores
>
> CMD:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/
> pfam_runner.pl --pep transdecoder.tmp.9643/longest_orfs.pep --pfam_db
> Pfam-A.hmm --CPU 48 -o Trinity.fasta.transdecoder.pfam.dat  --workdir
> transdecoder.tmp.9643  --debug
>
> Partitioning fasta file transdecoder.tmp.9643/longest_orfs.pep
>
> Processing with PFAM HMM searches...
>
> CMD: ParaFly -CPU 48 -c transdecoder.tmp.9643/parafly.sh --failed
> transdecoder.tmp.9643/parafly.sh.failed  -vv
>
> Can't exec "ParaFly": Too many levels of symbolic links at
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/
> pfam_runner.pl line 189.
>
> Error, cmd: ParaFly -CPU 48 -c transdecoder.tmp.9643/parafly.sh --failed
> transdecoder.tmp.9643/parafly.sh.failed  -vv  died with ret -1 at
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/
> pfam_runner.pl line 192.
>
> Error, cmd:
> /data5/Algae_RNAseq/FilterAssembly/Transdecoder/transdecoder_rel16JAN2014/
> pfam_runner.pl --pep transdecoder.tmp.9643/longest_orfs.pep --pfam_db
> Pfam-A.hmm --CPU 48 -o Trinity.fasta.transdecoder.pfam.dat  --workdir
> transdecoder.tmp.9643  --debug  died with ret 10240 at
> ../transdecoder_rel16JAN2014/TransDecoder line 498.
>
>
>
>
>
> So then I also tried to run TD and have it just make files for me to run
> PFAM searches myself as a separate command.  I submitted the following
> command:
>
> ../transdecoder_rel16JAN2014/TransDecoder -t Trinity.fasta -S
> --prepare_pfam
>
> And it seemed to just run through the whole TransDecoder run without
> stopping (generated final files).  Which file is supposed to be produced to
> search against Pfam?
>
>
>
> I get the same errors when using the Transdecoder packaged with Trinity
> releases as well.
>
>
>
> Thanks,
>
> Scott
>
>
>
>
>
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> --
> --
> Brian J. Haas
> The Broad Institute
> http://broad.mit.edu/~bhaas
>
>
>



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