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sbonisso / ig_graph

IgGraph performs VDJ classification of antibody reads
http://sbonisso.github.io/ig_graph/
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Probabilistic scoring not working? #1

Open sdwfrost opened 7 years ago

sdwfrost commented 7 years ago

Running ig_graph with the normal score works fine, but with the probabilistic score gives an error:

./iggraph -v IGHV.fas \
    -d IGHD.fas \
    -j IGHJ.fas \
    -V 21 \
    -D 10 \
    -J 21 \
    -s 1 \
    -t 2 \
    -f \
    -c \
    -m 3 \
    -r ./simple_indels_80_10000.fas \
    -o ./simple_indels_80_10000_s_iggraph.txt

gives:

READS = ./simple_indels_80_10000.fas
REFS =  IGHV.fas
OUTFILE =   ./simple_indels_80_10000_s_iggraph.txt
K = -1
K_v = 21    K_d = 10    J_k = 21
MAX REPORT =    3
NO CDR3 =   1
NUM THREAD =    2
SCORING = PROBABILISTIC
/home/simon/Programs/ig_graph/ext/seqan/basic/basic_exception.h:368 FAILED!  (Uncaught exception of type cereal::Exception: Failed to read 8 bytes from input stream! Read 0)
bash: line 13: 30235 Aborted                 (core dumped)

Running on Ubuntu 16.04, with data from here.

sbonisso commented 7 years ago

Hi Simon, That shouldn't be happening, I will check on it this weekend.

sbonisso commented 7 years ago

I was unable to reproduce the crash with the same parameters and read file. Are the reference input files IGHV.fas, IGHD.fas and IGHJ.fas available somewhere so that I may try to replicate all of your input arguments?

sdwfrost commented 7 years ago

Dear @sbonisso

Thanks for checking. The reference files are the same ones used for simulations (which are very similar to yours), and are available here.