#indoorevol metanalyses – fungi

Getting down to meta-analysis for the indoorevol project. Running Closed Ref OTU picking on Amazon Cloud, with a new fungi parameter file I compiled. Command ran:

pick_closed_reference_otus.py -i /home/ubuntu/data/fungi/Fungal_long_seqs.fasta -o /home/ubuntu/data/fungi/uclust_closedref_97 -r /home/ubuntu/data/fungi/its_12_11_otus/rep_set/99_otus.fasta -t /home/ubuntu/data/fungi/its_12_11_otus/taxonomy/99_otu_taxonomy.txt --parallel -O 8 -p /home/ubuntu/data/fungi/qiime_parameters_fungi.txt

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)