Bowtie2 index
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5 weeks ago
aranyak111 • 0

I am trying to build a Bowtie index from scratch. I have made a local installation of Bowtie in my cluster. The commands I have used to build a local index is "/gpfs/ycga/scratch60/nicoli/ag2646/Bowtie 2.4.2/bowtie2-2.4.2-linux-x86_64/"bowtie2-build "/gpfs/ycga/scratch60/nicoli/ag2646/Bowtie 2.4.2/bowtie2-2.4.2-linux-x86_64/genome.fa" human . The reference genome.fa is NCBI GrCHr38 build.

However, in place of 6 index files, I am getting only 4 .bt2 files but no rev.bt2 files. The terminal window shows Building a SMALL index Reading reference sizes

> Time reading reference sizes: 00:00:21 Calculating joined length
> Writing header Reserving space for joined string Joining reference
> sequences   Time to join reference sequences: 00:00:26 max according
> to bmaxDivN setting: 736462266 Using parameters --bmax 552346700 --dcv
> 1024   Doing ahead-of-time memory usage test   Passed!  Constructing
> with these parameters: --bmax 552346700 --dcv 1024 Constructing
> suffix-array element generator Building DifferenceCoverSample  
> Building sPrime   Building sPrimeOrder   V-Sorting samples.

How to generate all 6 index files to build a proper index.

seq RNA • 150 views
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Is that all output? The actual log from bowtie2 is hundreds of lines long. Maybe it crashed, how much memory is available on the machine, and did the job finish without errors? Yes, human genome is "small" in this context.

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The program did not crash and the shell script window display these information sit idly and ultimately just generate the 4 files.


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