Running bowtie2-2.2.3 to create an index

Question

[sumona88]

I installed bowtie2 following the instructions given on

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example

When running the example though, I get the following error

Settings:
  Output files: "lambda_virus.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /root/bowtie2-2.2.2.3/example/reference/lambda_virus.fa
Error: could not open /root/bowtie2-2.2.2.3/example/reference/lambda_virus.fa
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 /root/bowtie2-2.2.2.3/example/reference/lambda_virus.fa lambda_virus

What is a Bowtie exception?

Answer 1

[Sam]

The error is basically:

Error: could not open /root/bowtie2-2.2.2.3/example/reference/lambda_virus.fa

Which means it cannot find the file: /root/bowtie2-2.2.2.3/example/reference/lambda_virus.fa

You should check if you have that file in the path stated.