Re: [Transdecoder-users] Transdecoder running error

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

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