no matching bam/bai file found

[Juliana Chu]

Hello there,

I had a problem running my data with MAJIQ. Where in the command line :

majiq build /Users/ju.chu/BCB330/MAJIQ/bam -c /Users/ju.chu/BCB330/MAJIQ/test.init.txt -o /Users/ju.chu/BCB330/MAJIQ/out

and got an error saying :

RuntimeError: No matching bam (and bam.bai) or sj file was found matching the experiment D7K60d2_nucChr in any of the provided paths in the build configuration

however, the bam file:D7K60d2_nucChr.bam and bai file D7K60d2_nucChr.bam.bai is actually in the path /Users/ju.chu/BCB330/MAJIQ/bam

and this is my configuration file "test.init.txt" :

[info]

readlen=380

bamdirs=/Users/ju.chu/Desktop/BCB330/MAJIQ/bam

genome=araTha10

strandness=None

[experiments]

D7K=D7K60d2_nucChr

I wonder why MAJIQ cannot find my files, I have checked the path, and I had it running with the workshop example before. 

Please help me! Thank you !!!

[Anna-Leigh Brown]

The bandirs should be just a directory path like this:

bamdirs=/Users/ju.chu/Desktop/BCB330/MAJIQ/

And inside that folder you should have a file called 

D7K60d2_nucChr.bam

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[Juliana Chu]

Hello, thanks for the reply.

However, my bam files are in the bam directory which has a path bamdirs=/Users/ju.chu/Desktop/BCB330/MAJIQ/bam, and it does have the file D7K60d2_nucChr.bam. 

I have also tried to move the bam file into other folders and change the path in the configuration file, it still doesn't work.

Please help!

[Anna-Leigh Brown]

At a guess, (sorry I'm not actually a majiq developer or anything)

try

bamdirs=/Users/ju.chu/Desktop/BCB330/MAJIQ/bam/

with a backslash

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