A question on how abyss-pe manages to find the library files

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leonardo alves

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May 2, 2018, 6:10:25 PM5/2/18
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Hi there,
Sorry if that's a dumb question, but I would like to understand how Abyss look for the files whose paths I've included after "in=".
For example:
$ls temp/
test_r1.fq.gz test_r2.fq.gz
Then running:
$abyss-pe -C out j=12 name=nana k=46 in='temp/test_r1.fq.gz temp/test_r2.fq.gz'
Returns the error:
Reading `temp/test_r1.fq.gz'...
error: `temp/test_r1.fq.gz': No such file or directory
However, typing the full path returns no error and the assembly runs smootly.
$abyss-pe -C out j=12 name=nana k=46 in='/home/some_path_to/temp/test_r1.fq.gz /home/some_path_to/temp/test_r2.fq.gz'

I am running Abyss 2.0.3 in a bash shell.

Many thanks!

Ben Vandervalk

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May 2, 2018, 6:40:04 PM5/2/18
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Hi Leonardo,

When using relative paths, the paths must be relative to the `out` directory (because you used `-C out` in your command).  GNU make switches to the target directory first, then runs the assembly commands.

- Ben

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leonardo alves

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May 3, 2018, 8:19:37 AM5/3/18
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Hi Ben,
Think I got it. But does that mean I have to store the input files in the "out" directory when running?

Thanks

Ben Vandervalk

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May 3, 2018, 11:52:28 AM5/3/18
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Leonardo,

Not at all! It just means that your relative paths have to be written as if you were in the "out" directory.  Probably that just means adding an extra "../" in front of your paths.

IMO, it is simpler and better practice just to use absolute paths.

- Ben

leonardo alves

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May 3, 2018, 12:40:23 PM5/3/18
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That is alright. Thank you Ben!
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