Io_trace

This tool provides a simple wrapper around strace to monitor the amount of I/O performed by a tool.

I/O can be restricted to specific files with prefix or regexp pattern matching. It also displays I/O on sockets and stdin/stdout/stderr, but note that it cannot report how much I/O is performed on mmap()ed files.

Usage

Usage: io_trace [options] filename ... -- command argument ... e.g.: io_trace -x -p foo.bam -- samtools view foo.bam X:100-110

Options: -p prefix Only output filenames matching a specific prefix -r regexp Only output filenames matching a specific regexp -x Suppress files with no I/O performed on them -S Suppress stdin/stdout/stderr and sockets

Example

Comparing a CRAM file against a BAM file with samtools range query. We can clearly see BAM loads much more (the entirety infact) of the index, but less data from the BAM file itself due to a smaller block size although in 3 sections. CRAM loads only a small amount of the index, a larger (but single) data block from the cram file and an unknown amount of reference sequence via mmap.

BAM:

./io_trace -S -p /nfs -- samtools view /nfs/sam_scratch/jkb/data/NA20800.chrom20.ILLUMINA.bwa.TSI.low_coverage.20101123.bam 20:20000000-20000000

File: /nfs/sam_scratch/jkb/data/NA20800.chrom20.ILLUMINA.bwa.TSI.low_coverage.20101123.bam.bai
    Num. open           2
    Num. close          2
    Num. mmap           0
    Num. seeks          0
    Num. read           5
    Num. pread          0
    Num. sendto         0
    Num. write          0
    Num. pwrite         0
    Num. recvfrom       0
    Bytes read          179072
    Bytes written       0

File: /nfs/sam_scratch/jkb/data/NA20800.chrom20.ILLUMINA.bwa.TSI.low_coverage.20101123.bam
    Num. open           1
    Num. close          1
    Num. mmap           0
    Num. seeks          3
    Num. read           7
    Num. pread          0
    Num. sendto         0
    Num. write          0
    Num. pwrite         0
    Num. recvfrom       0
    Bytes read          196636
    Bytes written       0

CRAM:

$ ./io_trace -S -p /nfs -- samtools view /nfs/sam_scratch/jkb/data/NA20800.chrom20.ILLUMINA.bwa.TSI.low_coverage.20101123.cram 20:20000000-20000000

File: /nfs/srpipe_references/cram_cache/0d/ec/9660ec1efaaf33281c0d5ea2560f
    Num. open           1
    Num. close          1
    Num. mmap           1
    Num. seeks          2
    Num. read           0
    Num. pread          0
    Num. sendto         0
    Num. write          0
    Num. pwrite         0
    Num. recvfrom       0
    Bytes read          0
    Bytes written       0

File: /nfs/sam_scratch/jkb/data/NA20800.chrom20.ILLUMINA.bwa.TSI.low_coverage.20101123.cram.crai
    Num. open           2
    Num. close          2
    Num. mmap           0
    Num. seeks          0
    Num. read           3
    Num. pread          0
    Num. sendto         0
    Num. write          0
    Num. pwrite         0
    Num. recvfrom       0
    Bytes read          9725
    Bytes written       0

File: /nfs/sam_scratch/jkb/data/NA20800.chrom20.ILLUMINA.bwa.TSI.low_coverage.20101123.cram
    Num. open           1
    Num. close          1
    Num. mmap           0
    Num. seeks          1
    Num. read           8
    Num. pread          0
    Num. sendto         0
    Num. write          0
    Num. pwrite         0
    Num. recvfrom       0
    Bytes read          547188
    Bytes written       0