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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Max Planck Institute for Chemical Ecology
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