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– cp ~/r100609_1_thy__coreRag1__Rag1_E1.fastq .
– ~/src/bowtie2-2.1.0/bowtie2 -x ~/indexes/mm9 -
U r100609_1_thy__coreRag1__Rag1_E1.fastq -S
• Check the process status (execution time
,CPU, memory) with “ps” command for each
resident set size, the non-swapped physical memory that a task has used (in kiloBytes)
• Copy 1GB divided by 1 – 10 blocks
– for count in $(seq 1 10); do for directory in
uncompressed compressed; do dd if=/dev/zero
of=/mnt/$directory/foovar count=$count bs=`perl
-e "print int(1000000000 / $count - 0.5) + 1"`
2>&1 | tail -n1 | sed 's/^.*, //'; done; done | paste
- - > dd.txt &
Alignment test 1
• The test processes were terminated with memory error.
Out of memory allocating the offs array for the Bowtie index.
Please try again on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/ec2-user/src/bowtie2-2.1.0/bowtie2-align --
wrapper basic-0 -x indexes/mm9 -S
r100609_1_thy__coreRag1__Rag1_E1.1.sam --threads 1 -U
bowtie2-align exited with value 1
File system disk space usage (df)
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/xvde1 6193088 2393636 3736840 40% /
none 7619740 0 7619740 0% /dev/shm
tank/compressed 79563136 12784384 66778752 17% /mnt/compressed
tank/uncompressed 89918080 23139328 66778752 26% /mnt/uncompressed
tank 66778752 0 66778752 0% /tank
100GB disk pooling (64G + 13G + 23G)
• We adopted a short-read alignment step with bowtie2
to the tests of ZFS, as it would mainly utilize the
computational resource including storage disk.
• The tests show that there is no considerable difference
of resource usage between on uncompressed and
compressed disk partitions of ZFS.
– Execution time, CPU, memory, I/O performance
– But it may need more tests in more computational burden
to recognize the stability of ZFS.
• The adoption of compressed system makes more
efficient usage of our storage, especially with unzipped
data files. (refer slide 6-7)