Please help with newbie Bowtie2 question (Mac)!

[Bubblepig]

Hello everyone,

I've just downloaded "bowtie2-2.1.0-macos-x86_64.zip" on my mac. Put the unzipped file directly under Users/Behr.

The file seems to contain all necessary files:
(sequence.fasta is lambda phage sequence for practice).

Behrs-MacBook-Pro:bt2_home Behr$ ls -p
AUTHORS
LICENSE
MANUAL
MANUAL.markdown
MAPK10.fasta
NEWS
TUTORIAL
VERSION
bowtie2
bowtie2-align
bowtie2-align-debug
bowtie2-build
bowtie2-build-debug
bowtie2-inspect
bowtie2-inspect-debug
doc/
example/
scripts/
sequence.fasta

However when I ran the command, I got 2 error messages:
Behrs-MacBook-Pro:bt2_home Behr$ /Users/Behr/BT2_home/bowtie2-build /Users/Behr/BT2_home/sequence.fa blah
Settings:
Output files: "blah.*.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:
/Users/Behr/BT2_home/sequence.fa
Error: could not open /Users/Behr/BT2_home/sequence.fa
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/Behr/BT2_home/bowtie2-build /Users/Behr/BT2_home/sequence.fa blah

Can someone help me with this, please?

Thank you very much in advance!
Joyce

[liweixie]

The directory for your fa file may not be right. You can try ~/ to indicate your fa file direct

[Bubblepig]

Thank you, that fixed the problem - it's indeed the .fa! (should be .fasta).
Joyce :P