Error running usearch61

# run otu picking with usearch61

pick_open_reference_otus.py -i $PWD/SEQ/seqs.fna -o $PWD/OTU/ -r $REFSEQS -s 0.1 -m usearch61 -p $PWD/otu_settings.txt

Error running usearch61. Possible causes are unsupported version (current supported version is usearch v6.1.544) is installed or improperly formatted input file was provided

# check log file

cat OTU/step1_otus/abundance_sorted.log

usearch_i86linux32 v6.1.544, 4.0Gb RAM (8.1Gb total), 4 cores

°°°

---Fatal error---

Out of memory, mymalloc(34603016), curr 4.27e+09 bytes

Reason:

"Out of memory": number of sequences exceeds the 4GB memory limit of the 32 bit version of usearch61.

Work around:

Run pick_open_reference_otus.py without option "pick_otus:enable_rev_strand_match True" to half the memory usage.

Solution:

upgrade to a 64 bit version of usearch61 (not free)

read more

https://groups.google.com/forum/#!msg/qiime-forum/j3uFfAgGkCM/QgywlyYuOlUJ