Re-running Yatsunenko and GOM QIIME

Re-running the Yatsunenko et al. Core Analyses because the old run was open-reference OTU picking, and not the closed-ref protocol (my previous commmand didn’t turn off split libraries)

core_qiime_analyses.py -i /home/ubuntu/data_yatsunenko/ps_metagenome_extract/ps_metagenome_combined.fna -o /home/ubuntu/ps_metagenome_coreanalyses_7oct -m /home/ubuntu/qiime_ps_metagenomes_mappingfile.txt -f –suppress_split_libraries -t /home/ubuntu/gg_otus_4feb2011/trees/gg_97_otus_4feb2011.tre -p /home/ubuntu/qiime_parameters_metagenome_7Oct.txt –parallel

But for some reason alpha rarefaction didn’t work so had to run this script after getting error:

alpha_rarefaction.py -i /home/ubuntu/ps_metagenome_coreanalyses_7oct/otus/otu_table.biom -o /home/ubuntu/ps_metagenome_coreanalyses_7oct/alpha_rarefaction/ -t /home/ubuntu/ps_metagenome_coreanalyses_7oct/otus/rep_set.tre -m /home/ubuntu/qiime_ps_metagenomes_mappingfile.txt
ubuntu@ip-10-218-7-163:~$

**note, for parallel uclust_ref core analyses, you must delete from parameters file the following parameters: –clustering_algorithim, –max_e_value, and –max_cdhit_memory (all from pick_otus parameters) and –e_value (from assign_taxonomy using rep)

Also moving forward with more GOM QIIME-ing, using Closed and Open-ref based OTU picking. Going to use a bunch of different analyses, including uclust_ref and usearch_ref.

core_qiime_analyses.py -i /home/ubuntu/GOM_demultiplexed/GOM_concat_fwd_demulti_1to12_1.fna -o home/ubuntu/GOM_coreanalyses_ClosedRef_99_7Oct -m /home/ubuntu/QIIMEmappingfile_GOM_Illumina_fakebarcodes.txt -f –suppress_split_libraries -p /home/ubuntu/qiime_parameters_GOM_ClosedRef.txt –parallel

Also figured out why the PYNAST euk alignment wasn’t working – I had the align_seqs:min_length set to 150 originally, meaning that no Illumina sequence would ever align because they’re wayyy shorter than this. Now changed this parameter to 70 in all the aiime parameter files.

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