BLAST Dongying’s markers and RAxML run on thesis news

Making progress on BLASTing Dongying vs. Parfrey’s eukaryotic markers. Ran command on Edhar:

blastall -p blastp -d /home/hollybik/euks_vs_dongying_markers/DW_BacArch_ComboMarkers.faa -i /home/hollybik/Euks_ParfreyMarkers/Euk_ParfeyMarkers_allgenes_unaligned.fasta -o Parfrey_vs_Dongying_blastp.txt -v 3 -b 3

Having major problems with file conversions, so trying to run RAxML locally now on Edhar:

raxmlHPC -s SSUalign_BikThesisNems_Phylip_21Apr.txt -n SSUalign_RAxML_GTRCAT -m GTRCAT -f a -T 4

That didn’t work so Guillaume fixed the Phylip file and we ran the following command:

raxmlHPC -s gjospin_23Apr_out.phylip -n SSUalign_RAxML_GTRCAT -m GTRCAT -f a -T 4 -x 12345 -# 100 -p 12345

Also re-downloaded the newest version of PhyloSift (including all new markers), and re-ran the xeno_assembly_low_cov.fa

./phylosift all /home/hollybik/TestData/xeno_assembly_low_cov.fa

Parfrey Euk Markers – Accessions to GIs to Taxon IDs

Spent today wrestling with scripts to convert these damn accessions to GI numbers; Guillaume modified some of the BioPerl scripts using Bio::DB::Eutils modules. All listed in Edhar: /home/hollybik/eukmarkers_taxonids/accs_from_aligns/

Run the following commands to convert Accessions to GIs and then pull down NCBI taxon IDs (script prints text output with Accession GI NCBI_taxon with space between each)

perl gjospin_taxon_Acc_GI.pl Accs_14_3_3 Taxon_gi_14_3_3
perl gjospin_taxon_Acc_GI.pl Accs_40S Taxon_gi_40S
perl gjospin_taxon_Acc_GI.pl Accs_Actin Taxon_gi_Actin
perl gjospin_taxon_Acc_GI.pl Accs_Atub Taxon_gi_Atub
perl gjospin_taxon_Acc_GI.pl Accs_Btub Taxon_gi_Btub
perl gjospin_taxon_Acc_GI.pl Accs_ef1aLike Taxon_gi_ef1aLike
perl gjospin_taxon_Acc_GI.pl Accs_ef2 Taxon_gi_ef2
perl gjospin_taxon_Acc_GI.pl Accs_enolase Taxon_gi_enolase
perl gjospin_taxon_Acc_GI.pl Accs_gamma Taxon_gi_gamma
perl gjospin_taxon_Acc_GI.pl Accs_grc5 Taxon_gi_grc5
perl gjospin_taxon_Acc_GI.pl Accs_hsp70 Taxon_gi_hsp70
perl gjospin_taxon_Acc_GI.pl Accs_hsp70cyt Taxon_gi_hsp70cyt
perl gjospin_taxon_Acc_GI.pl Accs_hsp70er Taxon_gi_hsp70er
perl gjospin_taxon_Acc_GI.pl Accs_Hsp90 Taxon_gi_Hsp90
perl gjospin_taxon_Acc_GI.pl Accs_metk Taxon_gi_metk
perl gjospin_taxon_Acc_GI.pl Accs_Rad51 Taxon_gi_Rad51
perl gjospin_taxon_Acc_GI.pl Accs_rps22 Taxon_gi_rps22
perl gjospin_taxon_Acc_GI.pl Accs_Rps23a Taxon_gi_Rps23a
perl gjospin_taxon_Acc_GI.pl Accs_TFIIH Taxon_gi_TFIIH
perl gjospin_taxon_Acc_GI.pl Accs_Tsec61 Taxon_gi_Tsec61
perl gjospin_taxon_Acc_GI.pl Accs_U5 Taxon_gi_U5