Error with sample dataset (cannot find .bai)

[Former user]

Dear all. I am trying to run ROSE on a MAC (maverick) using the sample dataset provided with the code. The scripts runs fine until mapping. It states it cannot find the associated bai file (see below). I left all files in the same folder (from the Zipped downloadable folder). Any idea why this is happening? Sorry if this is obvious, I am bit of a Newbie.

PAUSING TO MAP {'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example_test/mappedGFF/HG18_MM1S_MED1_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': '/Users/lucamagnani/Downloads/ROSE_DATA', 'rpm': True, 'input': '/Users/lucamagnani/Downloads/ROSE_DATA'} ['2/data/MM1S_MED1.hg18.bwt.sorted.bam', '2/data/HG18_MM1S_MED1.gff'] {'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example_test/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': '/Users/lucamagnani/Downloads/ROSE_DATA', 'rpm': True, 'input': 'example_test/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff'} ['2/data/MM1S_MED1.hg18.bwt.sorted.bam'] ERROR: no associated .bai file found with bam. Must use a sorted bam with accompanying index file ERROR: no associated .bai file found with bam. Must use a sorted bam with accompanying index file Usage: ROSE_bamToGFF.py [options] -b [SORTED BAMFILE] -i [INPUTFILE] -o [OUTPUTFILE]

[luca magnani]

wscc-lmagnani:young_computation-rose-1a9bb86b5464 2 lucamagnani$ python ROSE_main.py -g HG18 -i /Users/lucamagnani/Downloads/ROSE_DATA\ 2/data/HG18_MM1S_MED1.gff -r /Users/lucamagnani/Downloads/ROSE_DATA\ 2/data/MM1S_MED1.hg18.bwt.sorted.bam -o example_test -s 12500 -t 2500

[charles_lin]

Hi Luca,

The command you are using to call ROSE is incorrect in several places. For instance, this path "/Users/lucamagnani/Downloads/ROSE_DATA\ 2/data/MM1S_MED1.hg18.bwt.sorted.bam" is incorrect and probably should be " /Users/lucamagnani/Downloads/ROSE_DATA/data/MM1S_MED1.hg18.bwt.sorted.bam"

Please refer to the example.sh or test.sh file to see a correct call of ROSE.

[luca magnani]

Thanks for the prompt reply, very stupid of me. Actually everything run fine (with sample dataset) after this easy fix. Now running my own data.

[luca magnani]

Hi Charles, a technical question. Can I run ROSE in parallel in multiple terminal tabs?

[Jared Andrews]

You can run it in multiple terminals, or you can follow their notes to parallelize it as shown below:

"This code can be easily parallelized by following the instructions in the main function of mapEnhancerFromFactor around line 369."