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gengit / PosiGene

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empty result tables #1

Closed astridboehne closed 7 years ago

astridboehne commented 7 years ago

Hi I installed PosiGen on a Unix cluster and the test run worked smoothly. Now I wanted to run it with two fish non homologen species and Danio rerio as the only fish homologen and outgroup. this is the command I used: perl /scicore/home/salzburg/boehne/applications/PosiGene-master/PosiGene.pl \ -nhsbr=Eretmodus_Female:/scicore/home/salzburg/eltaher/KissSplice/ecyanostictus_F_M/TransDec_F/Trinity.fasta.transdecoder.cds,$HOME/applications/PosiGene-master/data/Oreochromis_niloticus.gbk,$HOME/applications/PosiGene-master/data/Danio_rerio.gbk \ -ts=Eretmodus_Female \ -as=Oreochromis_niloticus \ -rs=$HOME/applications/PosiGene-master/data/Oreochromis_niloticus.gbk \ -o=$HOME/Ambizione/KaKs_transcriptomes/PosiGen/ecyanostictus_F/Orenil_anchor \ -tn=16 \ -t=$HOME/Ambizione/KaKs_transcriptomes/PosiGen/ecyanostictus_F/ErecyaF.nwk

I did run it without a tree first but got the error not enough information to build tree. So I added the species tree and everything seems to run fine, all files are created but the results table contain only the headers and nothing else I attach you all the log files and STDOUT, STDERR was empty Any help would be great logs.zip PosiGenEreF.o28336384.txt progress.txt

tianrenmao commented 7 years ago

I am a user of PosiGene. I suggest you simplify all your species name. For example, change Oreochromis_niloticus to "a". Also -rs had better be fed with fasta. All the fasta files had better end with ".fasta". You don't really need to provide a tree file. Tell me if it works.

astridboehne commented 7 years ago

Hi the solution was to shorten the sequence names in the transdecoder output file. Thanks Arne for helping!