[Transdecoder-users] Transdecoder running error

[Geib, S. <Sco...@AR...>]

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.pl transdecoder.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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