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#316 (ERR): Expected bowtie2 to be in same directory with bowtie2-align
I'm attempting to run bowtie2-2.2.3 on a Windows 7 machine using Cygwin. I downloaded bowtie2-2.2.3-mingw-win64.
I get the following error:
$ $BT2_HOME/bowtie2 -x lambda_virus -U $BT2_HOME/example/reads/reads_1.fq -S eg1.sam
(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
/Kesseli_Programs/bowtie2-2.2.3/
Exiting now ...
I haven't altered the contents of the unzipped folder bowtie2-2.2.3. They are:
$ ls
AUTHORS bowtie2-build-l-debug.exe example
bowtie2 bowtie2-build-s.exe LICENSE
bowtie2.bat bowtie2-build-s-debug.exe MANUAL
bowtie2-align-l.exe bowtie2-inspect MANUAL.markdown
bowtie2-align-l-debug.exe bowtie2-inspect.bat NEWS
bowtie2-align-s.exe bowtie2-inspect-l.exe scripts
bowtie2-align-s-debug.exe bowtie2-inspect-l-debug.exe TUTORIAL
bowtie2-build bowtie2-inspect-s.exe VERSION
bowtie2-build.bat bowtie2-inspect-s-debug.exe
bowtie2-build-l.exe doc
Am I doing something wrong? Any suggestions/comments would be greatly appreciated.
Hi Trudi,
We are no longer building bowtie2 for cygwin. The version you downlaoded is for mingw. You can try to build bowtie under cygwin but I would rather recommend setting up mingw instead.
Val
Hi Val,
Thank you for your quick response. Since I'm not trying to build from source (I was simply trying to call bowtie2 from with a Cygwin terminal window), am I correct in assuming that the Windows binary has some dependency on mingw? However, both before and after install MinGW I get the same error message when I attempt to run the example code from "Getting started with Bowtie 2: Lambda phage example" in the Windows command prompt window.
The forward files (lambda_virus.1-4.bt2), but not the reverse files, are generated. An error window pops up - "bowtie2-build-s.exe has stopped working A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available.".
The output -
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:4, size_t:8
Input files DNA, FASTA:
C:\Kesseli_Programs\bowtie2-2.2.3\example\reference\lambda_virus.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 12125
Using parameters --bmax 9094 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 9094 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Hi Trudi,
Your assumption is correct. There is one dependency on mingw. The precompiled mingw package shoul work assuming a 64bit mingw is installed. We recommend looking at mingw personal builds since those may save you some time. Rubenvb personal build is pretty good for example. Let us know if you manage to make it work.
val
This will be fixed in the next release since the Windows binaries will be statically linked.
Thank you for reporting this to us. It will be more conveniently address in the next release.
Val