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spond / IgSCUEAL

B-cell 454 processing
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AuxBF/MergeVRegionAlignments.bf doesn't read the directory #4

Closed sdwfrost closed 9 years ago

sdwfrost commented 9 years ago

I've checked and double-checked that I'm entering the directory right - both with and without the trailing forward slash, but the BF can't seem to find my alignments (named CDR3.fas.aligned etc.) (my directories are removed from the below output).

$ HYPHYMP AuxBF/MergeVRegionAlignments.bf
The directory containing V-region amino-acid alignments:/homo_sapiens/regions/
Error:
Could not find source dataset file:filesIn[fileID] Path stack: {/usr/local/lib/hyphy,AuxBF/}

Function call stack
1 : Read Data Set current from file filesIn[fileID]
-------
Segmentation fault
spond commented 9 years ago

Hi Simon,

I can't reproduce the error with your test data, if I supply the absolute path to the directory (e.g. /Volumes/sergei-raid/Coding/IgSCUEAL/test/issue4/), the script runs fine and generates a merged alignment and partition file.

Sergei

sdwfrost commented 9 years ago

Dear Sergei,

I get the following output on Mac OSX

HYPHYMP AuxBF/MergeVRegionAlignments.bf
The directory containing V-region amino-acid alignments:/Users/simon/Programs/IgSCUEAL/data/test/issue4
Loading /Users/simon/Programs/IgSCUEAL/data/test/issue4/FR1.fas.aligned
Error:
Could not find source dataset file:filesIn[0] Path stack: {/usr/local/lib/hyphy/,/Users/simon/IgSCUEAL/AuxBF/}

Function call stack
1 : Read Data Set first from file filesIn[0]
-------

It's finding the first file OK, but the path stack is clearly wrong. However, even when I create the /Users/simon/IgSCUEAL directory, I get the same error.

sdwfrost commented 9 years ago

Dear Sergei,

Oddness about the paths, but I updated HyPhy on my OSX box, and now this works on both my Linux box and OSX.

$ HYPHYMP AuxBF/MergeVRegionAlignments.bf
The directory containing V-region amino-acid alignments:/Users/simon/Programs/IgSCUEAL/test/issue4
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/FR1.fas.aligned
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/CDR1.fas.aligned
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/FR2.fas.aligned
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/CDR2.fas.aligned
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/FR3.fas.aligned
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/CDR3.fas.aligned
Loading /Users/simon/Programs/IgSCUEAL/test/issue4/J.fas.aligned

/Users/simon/Programs/IgSCUEAL/AuxBF/Write merged protein alignment to:/Users/simon/Programs/IgSCUEAL/test/V_region_aa.nex

Check messages.log details of this run.