QIIME GOM data

For some reason I couldn’t get the parallel_assign_taxonomy_rdp.py script to work, so I had to revert back to the normal assign_taxonomy.py script. I was getting an error unless I increased the max memory flag, so remember to do this again next time.

assign_taxonomy.py -m rdp -i /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set.fasta -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -t /home/ubuntu/Silva_108/taxa_mapping/Silva_RDP_taxa_mapping_Eukarya_only_genus.txt -o /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/rdp_genus_assigntaxon/ –rdp_max_memory 50000

assign_taxonomy.py -m rdp -i /home/ubuntu/GOM_demulti2_rev_OpenRef_uclust99_12Oct/GOM_concat_rev_demultirepeat_1to12_2_otus_rep_set.fasta -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -t /home/ubuntu/Silva_108/taxa_mapping/Silva_RDP_taxa_mapping_Eukarya_only_genus.txt -o /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/rdp_genus_assigntaxon/ –rdp_max_memory 50000

Making OTU tables of all seqs:

make_otu_table.py -i GOM_concat_fwd_demultirepeat_1to12_1_otus.txt -t rdp_genus_assigntaxon/GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set_tax_assignments.txt -o GOM_concat
_fwd_demultirepeat_1to12_1_otu_table_allotus.biom

Chimera checking (used parallell for actual data anlysis, but listing non-parallel script here for reference):

identify_chimeric_seqs.py -i GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set.fasta -t /home/ubuntu/Silva_108/taxa_mapping/Silva_RDP_taxa_mapping_Eukarya_only_genus.txt -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -o GOM_concat_fwd_demultirepeat_1to12_1_chimeric_seqs.txt -m blast_fragments

parallel_identify_chimeric_seqs.py -m blast_fragments -i GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set.fasta -t /home/ubuntu/Silva_108/taxa_mapping/Silva_RDP_taxa_mapping_Eukarya_only_genus.txt -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -o GOM_concat_fwd_demultirepeat_1to12_1_chimeric_seqs.txt -O 6

 

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