Cryptomycota BLAST against Deepsea MolEcology data

Figured I’d get a move on and BLAST some of the cryptomycota data to see if there was anything interesting in my deep sea OTU data.

Was running into a bit of trouble and kept hitting error like this:

[blastall] ERROR: SeqPortNew: lcl|OCTU5627 stop(321) >= len(264)
[blastall] ERROR: SeqPortNew: lcl|OCTU5627 stop(321) >= len(264)
[blastall] ERROR: SeqPortNew: lcl|OCTU33393 start(262) >= len(232)
[blastall] ERROR: SeqPortNew: lcl|OCTU33393 start(323) >= len(232)

But then I talked to Aaron and he said I was formatting the DB with -p T (parsing with an index), which was giving me that problem. So in the end I formatted the DB with the command:

formatdb -i OTUrepset_uclust99_bothloci -p F -o F

And then the error went away and I was successfully able to run the Cryptomycota comparison:

megablast -d /home/hollybik/BLAST_db/99_QIIME_OTU_deepsea/OTUrepset_uclust99_bothloci -i /home/hollybik/BLAST_db/99_QIIME_OTU_deepsea/Cryptomycota_rRNAseq_Jones_2011_mod.txt -o cryptomycota_Deepsea_BLAST_3.txt -v 5 -b 5 -D 2

Where -v is the number of db matches, -b is the number of alignments to show, and -D is the output format (standard BLAST)

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