error with csv file implementation

[michelle171]

I attempted to replicate the csv fizzy implementation example, which included replicating the test documents. I received this error after the same command line call as shown in the example:

fizzy -n 2 -l Class -f MIM -m test.map -i test.csv -s -o test.ouput -r test.biom -v
usage: fizzy [-h] [-n SELECT] [-q BINS] -l LABEL [-f FS_METHOD] -i INPUT_FILE
[-m MAP_FILE] [-j] -o OUTPUT_FILE [-r OUTPUT_BIOM] [-v]
fizzy: error: unrecognized arguments: -s

When I took out the -s flag, I received this:
fizzy -n 2 -l Class -f MIM -m test.map -i test.csv -o test.ouput -r test.biom -v
Segmentation fault (core dumped)

I compiled all of the dependencies before trying this example, therefore I am not sure what is going wrong.

[gditzler]

Are test.{csv,biom} files that you created? A segmentation fault is likely going to be caused by an issue on the MIToolbox or FEASTtoolbox.

comiple with debugging flags, run it through gdb

…

On 4 August 2017 at 13:46, michelle171 ***@***.***> wrote: Yes I created those files, replicated from the example for csv files. I compiled both of those according to their instructions, do you have any suggestions? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAO2a68gVDoxFTBn7d7Ni5AEGmgm7Hcbks5sU1kGgaJpZM4Ot-h_> .

[yangfenglong]

I attempted to replicate the csv fizzy implementation example, which included replicating the test documents. I received this error after the same command line call as shown in the example:

fizzy -n 2 -l Class -f MIM -m test.map -i test.csv -s -o test.ouput -r test.biom -v
usage: fizzy [-h] [-n SELECT] [-q BINS] -l LABEL [-f FS_METHOD] -i INPUT_FILE
[-m MAP_FILE] [-j] -o OUTPUT_FILE [-r OUTPUT_BIOM] [-v]
fizzy: error: unrecognized arguments: -s

When I took out the -s flag, I received this:
fizzy -n 2 -l Class -f MIM -m test.map -i test.csv -o test.ouput -r test.biom -v
Segmentation fault (core dumped)

I compiled all of the dependencies before trying this example, therefore I am not sure what is going wrong.

I faced the seam problem with the test data :
https://github.com/gditzler/DataCollections/blob/master/AmericanGut/AmericanGut-Gut-Sex.biom
https://github.com/gditzler/Fizzy/blob/master/test/Tutorial.md