Dear Galaxy developers,
I am using a locally installed galaxy system. I have tested many
different function, it works pretty well. But now i am having a problem
with NGS tools.
I have installed bowtie2 and tophat2 etc locally, but when i run
bowtie to align the short reads to reference genome (selected from
history), it does not work, just shows waiting for running. I then
checked the files from bowtie2_wrapper.py with my own files as following
under command line:
python2.7 bowtie2_wrapper.py --num-threads=4 --output=test.out
--own-file=Nagenome.fasta --input1=control_R1.fq --input2=control_R2.fq
However, it didn't run well, it shows following error message:
Settings:
Output files: "/tmp/tmplBdrjc/Nagenome.*.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:
Nagenome.fasta
Total time for call to driver() for forward index: 00:00:00
Error indexing reference sequence
Error: could not open Nagenome.fasta
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build -f Nagenome.fasta /tmp/tmplBdrjc/Nagenome
I also tested with pre-build reference genome index, it worked well. So,
i guess there is something wrong with building index. However, i
couldn't figure out what could be the reason. The genome size is pretty
small, only 2000 sequences.
I am looking forward to hearing your feedback and helps.
best wishes,
Shuqing
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Department of Molecular Ecology
Max Planck Institute for Chemical Ecology
Hans-Knöll-Straße 8
D-07745 Jena Germany
E-mail: sxu(a)ice.mpg.de
Phone:+49 (0)3641 57 1129
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