Hi Arne
I have noticed something worrying: I have changed the version of posigen and ran the same command.
With my settings PosiGen only created very few alignments. When going through th elog files I figured that this might be due to the fact that at some step it is generating blasts/searches against the HomologDatabases that come with PosiGen and kicks out sequences based on this, however I never wanted to include sequence alignmnets against these species in the first place.
Was there a change that by default PosiGen tests again these species? I did not change my command, just the versions used, my data directory contains only two custom gbk datasets
here is the command and the beginning of the strange section from the log file:
perl /scicore/home/salzburg/boehne/applications/PosiGenNewVersion/PosiGene-master/PosiGene.pl \
-nhsbr=Aburtoni:/scicore/home/salzburg/eltaher/dev_stages/PosiGen/data/CD_HIT_Astbur3.0_Hybrid_reference_PosigenHeaders.fasta,/scicore/home/salzburg/boehne/applications/PosiGenNewVersion/PosiGene-master/data/Oreochromis_niloticus.gbk,/scicore/home/salzburg/boehne/applications/PosiGenNewVersion/PosiGene-master/data/Danio_rerio.gbk \
-ts=Aburtoni \
-as=Oreochromis_niloticus \
-rs=$HOME/applications/PosiGenNewVersion/PosiGene-master/data/Oreochromis_niloticus.gbk \
-o=$HOME/Ambizione/PosiGenAstbuDev/new_reference_052018 \
-tn=8 \
-t=$HOME/Ambizione/PosiGenAstbuDev/AstburOrenilDanrer.nwk \
-branch_name=Aburtoni \
-min_seq_num_soft=3 \
-blast_threshold=1E-03 \
-min_ident=60
and then here what Posigen is doing and was not doing before:
FindBestOrthologs_Oreochromis_niloticus.log
Aburtoni-Anolis_carolinensis: 57.9957356076759%
Aburtoni-Danio_rerio: 67.893369921015%
Aburtoni-Ictalurus_punctatus: 74.7524752475248%
Aburtoni-Mus_musculus: 68.4619019921477%
Aburtoni-Oreochromis_niloticus: 91.6542405432865%
Aburtoni-Xenopus_tropicalis: 57.8260869565217%
Anolis_carolinensis-Danio_rerio: 58.0412923736646%
Anolis_carolinensis-Oreochromis_niloticus: 56.766815274278%
Anolis_carolinensis-Xenopus_tropicalis: 62.5779625779626%
Danio_rerio-Ictalurus_punctatus: 77.9904306220096%
Danio_rerio-Mus_musculus: 74.4241706161137%
Danio_rerio-Oreochromis_niloticus: 70.0658197415012%
Danio_rerio-Takifugu_rubripes: 72.8476821192053%
Danio_rerio-Xenopus_tropicalis: 57.210401891253%
Ictalurus_punctatus-Oreochromis_niloticus: 74.0384615384615%
Mus_musculus-Oreochromis_niloticus: 73.7238696576891%
Oreochromis_niloticus-Oryzias_latipes: 51.3157894736842%
Oreochromis_niloticus-Takifugu_rubripes: 78.3333333333333%
Oreochromis_niloticus-Xenopus_tropicalis: 57.8260869565217%
Thanks for any advice how to turn that behavior of again
Best
Astrid
Hi Arne I have noticed something worrying: I have changed the version of posigen and ran the same command. With my settings PosiGen only created very few alignments. When going through th elog files I figured that this might be due to the fact that at some step it is generating blasts/searches against the HomologDatabases that come with PosiGen and kicks out sequences based on this, however I never wanted to include sequence alignmnets against these species in the first place. Was there a change that by default PosiGen tests again these species? I did not change my command, just the versions used, my data directory contains only two custom gbk datasets here is the command and the beginning of the strange section from the log file: perl /scicore/home/salzburg/boehne/applications/PosiGenNewVersion/PosiGene-master/PosiGene.pl \ -nhsbr=Aburtoni:/scicore/home/salzburg/eltaher/dev_stages/PosiGen/data/CD_HIT_Astbur3.0_Hybrid_reference_PosigenHeaders.fasta,/scicore/home/salzburg/boehne/applications/PosiGenNewVersion/PosiGene-master/data/Oreochromis_niloticus.gbk,/scicore/home/salzburg/boehne/applications/PosiGenNewVersion/PosiGene-master/data/Danio_rerio.gbk \ -ts=Aburtoni \ -as=Oreochromis_niloticus \ -rs=$HOME/applications/PosiGenNewVersion/PosiGene-master/data/Oreochromis_niloticus.gbk \ -o=$HOME/Ambizione/PosiGenAstbuDev/new_reference_052018 \ -tn=8 \ -t=$HOME/Ambizione/PosiGenAstbuDev/AstburOrenilDanrer.nwk \ -branch_name=Aburtoni \ -min_seq_num_soft=3 \ -blast_threshold=1E-03 \ -min_ident=60
and then here what Posigen is doing and was not doing before: FindBestOrthologs_Oreochromis_niloticus.log Aburtoni-Anolis_carolinensis: 57.9957356076759% Aburtoni-Danio_rerio: 67.893369921015% Aburtoni-Ictalurus_punctatus: 74.7524752475248% Aburtoni-Mus_musculus: 68.4619019921477% Aburtoni-Oreochromis_niloticus: 91.6542405432865% Aburtoni-Xenopus_tropicalis: 57.8260869565217% Anolis_carolinensis-Danio_rerio: 58.0412923736646% Anolis_carolinensis-Oreochromis_niloticus: 56.766815274278% Anolis_carolinensis-Xenopus_tropicalis: 62.5779625779626% Danio_rerio-Ictalurus_punctatus: 77.9904306220096% Danio_rerio-Mus_musculus: 74.4241706161137% Danio_rerio-Oreochromis_niloticus: 70.0658197415012% Danio_rerio-Takifugu_rubripes: 72.8476821192053% Danio_rerio-Xenopus_tropicalis: 57.210401891253% Ictalurus_punctatus-Oreochromis_niloticus: 74.0384615384615% Mus_musculus-Oreochromis_niloticus: 73.7238696576891% Oreochromis_niloticus-Oryzias_latipes: 51.3157894736842% Oreochromis_niloticus-Takifugu_rubripes: 78.3333333333333% Oreochromis_niloticus-Xenopus_tropicalis: 57.8260869565217%
Thanks for any advice how to turn that behavior of again Best Astrid