search

calico / basenji

Sequential regulatory activity predictions with deep convolutional neural networks.
Apache License 2.0
410 stars 126 forks source link

Error in running basenji_data.py #134

Open luohaitaofujian opened 2 years ago

luohaitaofujian commented 2 years ago

Hello!When I run the basenji_data.py,I met some problems. python basenji_data.py -d .1 -g data/unmap_macro.bed -l 196608 --local -o data/heart_l131k -p 8 -t .1 -v .1 -w 128 data/test.fna data/heart_wigs.txt (the test.fna is a bacteria genome)

stride_train 1 converted to 196608.000000 stride_test 1 converted to 196608.000000 Contigs divided into Train: 15 contigs, 7856972 nt (1.0000) Valid: 0 contigs, 0 nt (0.0000) Test: 0 contigs, 0 nt (0.0000) python basenji_data_read.py -w 128 -u sum -c 0.000000 -s 1.000000 data/out.bw data/heart_l131k/sequences.bed data/heart_l131k/seqs_cov/0.h5 Traceback (most recent call last): File "/root/luoht/preprocess/basenji_data.py", line 951, in main() File "/root/luoht/preprocess/basenji_data.py", line 421, in main fold_set_start = fold_set_indexes[0] IndexError: list index out of range

1.Why the valid and test are 0 contigs? 2.How can I deal with the indexerror?

Thank you!

davek44 commented 2 years ago

It looks like you're providing a FASTA file that doesn't match the BED file data/unmap_macro.bed or the BigWig files in data/heart_wigs.txt