bed file is not formed in the output directory.

[arthasking123]

Hi, I runned all the script in the README.md using the GLORI data, and failed to get the bed file in the output directory at last.

Here is the log:

Running RODAN basecaller
500 reads processed
1000 reads processed
1500 reads processed
2000 reads processed
2500 reads processed
3000 reads processed
3500 reads processed
4000 reads processed
4500 reads processed
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21500 reads processed
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37500 reads processed
38000 reads processed
38500 reads processed
39000 reads processed
39500 reads processed
40000 reads processed
40500 reads processed
Total 40578 reads
Finished in 1469.0 mins
[samfaipath] build FASTA index...
[M::mm_idx_gen::5.0210.81] collected minimizers
[M::mm_idx_gen::5.8921.42] sorted minimizers
[M::main::5.8921.42] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::6.1501.40] mid_occ = 422
[M::mm_idx_stat] kmer size: 14; skip: 5; is_hpc: 0; #seq: 1
[M::mm_idx_stat::6.3491.39] distinct minimizers: 20203919 (56.71% are singletons); average occurrences: 2.607; average spacing: 2.962
[M::worker_pipeline::20.1816.33] mapped 40578 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 --secondary=no -ax splice -uf -k14 -t 36 --cs /home/huajin/mafia/mAFiA/data/GRCh38_96.X.fa /home/huajin/mafia/mAFiA/output/rodan.fasta
[M::main] Real time: 20.215 sec; CPU: 127.844 sec; Peak RSS: 7.359 GB

=========================================================
ref_file : /home/huajin/mafia/mAFiA/data/GRCh38_96.X.fa
max_num_reads : 1000
min_coverage : 50
enforce_ref_5mer : False
backbone_model_path : /home/huajin/mafia/mAFiA/models/RODAN_HEK293_IVT.torch
extraction_layer : convlayers.conv21
feature_width : 0
classifier_type : logistic_regression
classifier_model_dir : /home/huajin/mafia/mAFiA/models/classifiers
bam_file : /home/huajin/mafia/mAFiA/output/minimap.q50.bam
fast5_dir : /home/huajin/mafia/mAFiA/data/fast5_chrX
out_dir : /home/huajin/mafia/mAFiA/output
batchsize : 2048
features_file : None
mod_file : /home/huajin/mafia/mAFiA/data/GLORI_chrX.bed
mod_prob_thresh : 0.5

Starting with fast5
Loading data test
Indexing fast5 files from /home/huajin/mafia/mAFiA/data/fast5_chrX
100%|██████████| 11/11 [00:12<00:00, 1.14s/it]
40578 reads indexed
Building dictionary of reads to mapped references
Finding my backbone...
Using device cpu, model RODAN_HEK293_IVT.torch at extraction layer convlayers.conv21
Parsing genome reference GRCh38_96.X.fa...
Loading motif classifiers...
Target motifs:
100%|██████████| 7004/7004 [00:00<00:00, 44903.09it/s]
Total 0 mod. sites written to /home/huajin/mafia/mAFiA/output/mAFiA.sites.bed
Total 40630 mod. reads written to /home/huajin/mafia/mAFiA/output/mAFiA.reads.bam
Finished in 0.3 mins

here is the file list of the output directory:

[arthasking123]

@ADHDrian

[ADHDrian]

Hi @arthasking123 , could you please check if your /home/huajin/mafia/mAFiA/models/classifiers contains the 5mer models?