denovo_abundance_sorted.fna was a fasta with the representative sequences
$ pick_otus.py -i NE9_chimera_usearch61/non_chimeras.fasta -m usearch61 -s 0.99 --de_novo_chimera_detection -k -x -o NE9_pickOTU99/
abundance_sorted.log denovo_smallmem_clustered.uc smallmem_clustered.log
denovo_abundance_sorted.fna non_chimeras_otus.log
denovo_abundance_sorted.uc non_chimeras_otus.txt
But the analysis runs to completion as far as I can tell. Any insight?
K
$ head non_chimeras_otus.txt
denovo236824 DimBioDivNE9_860622
denovo236825 DimBioDivNE9_860624 DimBioDivNE9_859747
denovo236826 DimBioDivNE9_860609
denovo236827 DimBioDivNE9_860617
denovo236820 DimBioDivNE9_860595
denovo236821 DimBioDivNE9_860588
denovo236822 DimBioDivNE9_860577
denovo236823 DimBioDivNE9_860621
denovo15142 DimBioDivNE9_1601741 DimBioDivNE9_1597207 DimBioDivNE9_1618319 DimBioDivNE9_1625072 DimBioDivNE9_1302067 DimBioDivNE9_1270107 DimBioDivNE9_1268528
[kturk@thalassa NE9_pickOTU99]$ head non_chimeras_otus.log
Usearch610DeNovoOtuPicker parameters:
Application:usearch61
minlen:64
output_dir:NE9_pickOTU99/
percent_id:0.99
remove_usearch_logs:False
rev:False
save_intermediate_files:True
sizeorder:False
threads:1
drwxrwxr-x 6 kturk kturk 4.0K Jan 25 19:32 ..
-rw-rw-r-- 1 kturk kturk 49M Jan 25 16:41 non_chimeras_otus.txt
drwxrwxr-x 2 kturk kturk 4.0K Jan 25 16:41 .
-rw-rw-r-- 1 kturk kturk 351 Jan 25 16:41 non_chimeras_otus.log
-rw-rw-r-- 1 kturk kturk 3.0K Jan 25 16:41 smallmem_clustered.log
-rw-rw-r-- 1 kturk kturk 75M Jan 25 16:41 denovo_smallmem_clustered.uc
-rw-rw-r-- 1 kturk kturk 1.7K Jan 25 16:16 abundance_sorted.log
-rw-rw-r-- 1 kturk kturk 160M Jan 25 16:16 denovo_abundance_sorted.uc
-rw-rw-r-- 1 kturk kturk 362M Jan 25 16:15 denovo_abundance_sorted.fna