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

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