Aligning seqs on iMac

While waiting for cloud support, running the 18S_chimera workflow on my iMac:

Parallel align sequences:

parallel_align_seqs_pynast.py -i /Users/hollybik/Desktop/Data/18S_chimera/AWS_analyses/18S_chimera_openref99_alldenovo_20Oct13/rep_set.fna -o /Users/hollybik/Desktop/Data/18S_chimera/AWS_analyses/18S_chimera_openref99_alldenovo_20Oct13/pynast_aligned_seqs -T --jobs_to_start 2 --template_fp /macqiime/silva_111/eukaryotes_only/rep_set_aligned_euks/99_Silva_111_rep_set_euk_aligned.fasta --pairwise_alignment_method uclust --min_percent_id 70.0 --min_length 150

Filter alignment:

filter_alignment.py -o /Users/hollybik/Desktop/18S_fallanalyses/GOM_Illumina/uclust_openref96_rev_27Aug/pynast_aligned_seqs -i /Users/hollybik/Desktop/18S_fallanalyses/GOM_Illumina/uclust_openref96_rev_27Aug/pynast_aligned_seqs/rep_set_aligned.fasta --allowed_gap_frac 0.999999 --threshold 3.0 --suppress_lane_mask_filter

Make Tree:

make_phylogeny.py -i /Users/hollybik/Desktop/18S_fallanalyses/18S_chimera/18S_chimera_openref96_alldenovo_18Oct13/pynast_aligned_seqs/rep_set_aligned_pfiltered.fasta -o /Users/hollybik/Desktop/18S_fallanalyses/18S_chimera/18S_chimera_openref96_alldenovo_18Oct13/rep_set.tre --root_method tree_method_default --tree_method fasttree

Also making progress with GOM_Illumina data that my desktop/laptop machines can handle:

parallel_align_seqs_pynast.py -i /Users/hollybik/Desktop/18S_fallanalyses/GOM_Illumina/uclust_openref96_rev_27Aug/rep_set.fna -o /Users/hollybik/Desktop/18S_fallanalyses/GOM_Illumina/uclust_openref96_rev_27Aug/pynast_aligned_seqs -T --jobs_to_start 2 --template_fp /macqiime/silva_111/eukaryotes_only/rep_set_aligned_euks/99_Silva_111_rep_set_euk_aligned.fasta --pairwise_alignment_method uclust --min_percent_id 70.0 --min_length 50
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