All fast5 files failed when perform call_mods #35
Description
Hi, very good software! Running multi_to_single_fast5, guppy_basecaller and tombo are all normal, but when running call_mods, it shows that all files fail. Whether it is the test data you provided or my own data. I have encountered this problem. The following is the code I run my own data and the corresponding log. I also set HDF5_PLUGIN_PATH as you said, but it doesn't work. For the test data, I also tried to unzip the file as issues #8, but the same problem still occurs. Thank you for your response.
data fractionation
multi_to_single_fast5 -i multi_read_fast5_dir -s fast5s/ -t 10 --recursive
guppy_basecaller
singularity exec /public/home/yxlong/Singularity/guppy-gpu.sif guppy_basecaller -i /public/home/yxlong/Modifications/HW04/fast5s/ -r -s fast5s_guppy --config dna_r9.4.1_450bps_hac_prom.cfg --device CUDA:0
config file: /opt/ont/guppy/data/dna_r9.4.1_450bps_hac_prom.cfg
model file: /opt/ont/guppy/data/template_r9.4.1_450bps_hac_prom.jsn
input path: /public/home/yxlong/Modifications/HW04/fast5s/
save path: fast5s_guppy
chunk size: 2000
chunks per runner: 1024
minimum qscore: 9
records per file: 4000
num basecallers: 4
gpu device: CUDA:0
kernel path:
runners per device: 20
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Found 4000 input read files to process.
Init time: 1776 ms
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
Caller time: 20067 ms, Samples called: 87639365, samples/s: 4.36734e+06
Finishing up any open output files.
Basecalling completed successfully.
tombo
cat fast5s_guppy/*/*fastq > fast5s_guppy.fastq
micromamba run -n ont-tombo tombo preprocess annotate_raw_with_fastqs --fast5-basedir /public/home/yxlong/Modifications/HW04/fast5s/ --fastq-filenames fast5s_guppy.fastq --sequencing-summary-filenames /public/home/yxlong/Modifications/HW04/fast5s_guppy/sequencing_summary.txt --basecall-group Basecall_1D_000 --basecall-subgroup BaseCalled_template --overwrite --processes 10
[10:19:15] Getting read filenames.
[10:19:15] Parsing sequencing summary files.
[10:19:15] Annotating FAST5s with sequence from FASTQs.
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4000/4000 [00:00<00:00, 7867.41it/s]
[10:19:15] Added sequences to a total of 4000 reads.
micromamba run -n ont-tombo tombo resquiggle /public/home/yxlong/Modifications/HW04/fast5s/ /public/home/jyli/HiFi_Genomes/03.AD1_Updated/HC04_V2/HC04_chr_adjust.fa --processes 10 --corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000 --overwrite
[10:21:21] Loading minimap2 reference.
[10:22:10] Getting file list.
[10:22:10] Loading default canonical ***** DNA ***** model.
[10:22:13] Re-squiggling reads (raw signal to genomic sequence alignment).
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4000/4000 [01:49<00:00, 36.43it/s]
[10:24:03] Final unsuccessful reads summary (2.6% reads unsuccessfully processed; 104 total reads):
1.4% ( 56 reads) : Poor raw to expected signal matching (revert with tombo filter clear_filters)
0.8% ( 31 reads) : Alignment not produced
0.4% ( 16 reads) : Read event to sequence alignment extends beyond bandwidth
0.0% ( 1 reads) : Fewer changepoints found than requested
[10:24:03] Saving Tombo reads index to file.
deepsignal_plant
micromamba run -n deepsignal deepsignal_plant call_mods --input_path /public/home/yxlong/Modifications/HW04/fast5s/ --model_path /public/home/yxlong/Modifications/example/model.dp2.CNN.arabnrice2-1_120m_R9.4plus_tem.bn13_sn16.both_bilstm.epoch6.ckpt --result_file fast5s.C.call_mods.tsv --corrected_group RawGenomeCorrected_000 --motifs C --nproc 10 --nproc_gpu 10
===============================================
parameters:
input_path:
/public/home/yxlong/Modifications/HW04/fast5s/
f5_batch_size:
30
model_path:
/public/home/yxlong/Modifications/example/model.dp2.CNN.arabnrice2-1_120m_R9.4plus_tem.bn13_sn16.both_bilstm.epoch6.ckpt
model_type:
both_bilstm
seq_len:
13
signal_len:
16
layernum1:
3
layernum2:
1
class_num:
2
dropout_rate:
0
n_vocab:
16
n_embed:
4
is_base:
yes
is_signallen:
yes
batch_size:
512
hid_rnn:
256
result_file:
fast5s.C.call_mods.tsv
gzip:
False
recursively:
yes
corrected_group:
RawGenomeCorrected_000
basecall_subgroup:
BaseCalled_template
is_dna:
yes
normalize_method:
mad
motifs:
C
mod_loc:
0
region:
None
positions:
None
reference_path:
None
nproc:
10
nproc_gpu:
10
===============================================
[main] call_mods starts..
cuda availability: False
4000 fast5 files in total..
parse the motifs string..
read_fast5 process-185516 starts
read_fast5 process-185518 starts
read_fast5 process-185517 starts
read_fast5 process-185519 starts
read_fast5 process-185520 starts
read_fast5 process-185521 starts
read_fast5 process-185522 starts
call_mods process-185523 starts
call_mods process-185524 starts
write_process-185525 starts
read_fast5 process-185516 ending, proceed 600 fast5s
read_fast5 process-185518 ending, proceed 570 fast5s
read_fast5 process-185522 ending, proceed 540 fast5s
read_fast5 process-185519 ending, proceed 510 fast5s
read_fast5 process-185521 ending, proceed 580 fast5s
read_fast5 process-185517 ending, proceed 600 fast5s
read_fast5 process-185520 ending, proceed 600 fast5s
call_mods process-185524 ending, proceed 0 feature-batches(512)
call_mods process-185523 ending, proceed 0 feature-batches(512)
write_process-185525 finished
4000 of 4000 fast5 files failed..