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tlemane / kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections
GNU Affero General Public License v3.0
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documentation, examples problems #28

Open EricDeveaud opened 11 months ago

EricDeveaud commented 11 months ago

Hello

after compiling kmindex from sources. I tried to run the example scripts. 1_buildsh -> OK 2_register.sh -> FAILURE see:

rpm_maker:examples/data > sh 2_register.sh
[2023-10-11 13:45:08.390] [error] [InvalidParamError] -> Unknown param: --index.
[2023-10-11 13:45:08.394] [error] [InvalidParamError] -> Unknown param: --index.

and when I try to use the doc eg here also have a problem.

rpm_maker:examples/data > kmindex build --fof fof1.txt --run-dir D1_index --index ./G --register-as D1 --hard-min --kmer-size 25 --bloom-size 1000000
[2023-10-11 13:49:11.338] [error] [MissingValueError] -> --hard-minneeds a value.

can you provide runnable instructions please.

regards

Eric

tlemane commented 10 months ago

Hello Thank you for pointing this out. I have updated the documentation and the examples. You should be able to follow the pipeline now. Teo