not working on EC2

The script finished for GOM Illumina reverse reads clustered at 96% – however – the script was not working…the log file indicated the script had been executed, but top command showed nothing running. Tried running the script manually (below command), both with and without the -T flag. Also didn’t seem to work – the paralell jobs would start but then would all end for some reason.. -i /home/ubuntu/gom_data/uclust_openref96_ref_27Aug/rep_set.fna -o /home/ubuntu/gom_data/uclust_openref96_ref_27Aug/pynast_aligned_seqs_manual -O 8 -t /home/ubuntu/gom_data/99_Silva_111_rep_set_euk_aligned.fasta -a uclust -p 70.0

So instead of worrying about that for now, I’m going to move on to 99% clustering on the reverse reads to see how long this takes. (note: the 96% cutoff finished overnight, for a ~1.5GB file on an m2.4xlarge instance) -i /home/ubuntu/gom_data/GOM_concat1.7_rev_demulti_1to12_2.fna -o /home/ubuntu/gom_data/uclust_openref99_28Aug -r /home/ubuntu/gom_data/99_Silva_111_rep_set_euk.fasta --parallel -O 10 -s 0.1 -p /home/ubuntu/gom_data/qiime_parameters_uclust99gom_aws28Aug.txt --prefilter_percent_id 0.0

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