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