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PengNi / ccsmeth

Detecting DNA methylation from PacBio CCS reads
BSD 3-Clause Clear License
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empty output of ccsmeth extract command #8

Closed tiramisutes closed 2 years ago

tiramisutes commented 2 years ago

Dear, Firstly, I align the subreads to genome using ccsmeth align and the output is input into ccsmeth extract as follows. But I get empty file m64081.pbmm2.features.zscore.fb.depth1.tsv and without any error stdout. The bam file input into ccsmeth align is output using the command ccs input output --hifi-kinetics.

ccsmeth extract --input m64081.pbmm2.bam --ref genome.fasta --threads 1 --norm zscore --comb_strands --depth 1 --output m64081.pbmm2.features.zscore.fb.depth1.tsv

And, the stdout is shown as follows:

# ===============================================
## parameters: 
input:
    m64081.pbmm2.bam
ref:
    genome.fasta
holeids_e:
    None
holeids_ne:
    None
output:
    m64081.pbmm2.features.zscore.fb.depth1.tsv
seq_len:
    21
motifs:
    CG
mod_loc:
    0
methy_label:
    1
mapq:
    20
identity:
    0.8
two_strands:
    False
comb_strands:
    True
depth:
    1
norm:
    zscore
no_decode:
    False
num_subreads:
    0
path_to_samtools:
    None
holes_batch:
    50
seed:
    1234
threads:
    10
# ===============================================
[extract_features]start..
extrac_features process-370857 starts
extrac_features process-370857, 200 hole_batches(50) proceed
extrac_features process-370866 starts
extrac_features process-370866, 200 hole_batches(50) proceed
extrac_features process-370863 starts
extrac_features process-370863, 200 hole_batches(50) proceed
extrac_features process-370864 starts
extrac_features process-370864, 200 hole_batches(50) proceed
extrac_features process-370861 starts
extrac_features process-370861, 200 hole_batches(50) proceed
extrac_features process-370865 starts
extrac_features process-370865, 200 hole_batches(50) proceed
extrac_features process-370860 starts
extrac_features process-370860, 200 hole_batches(50) proceed
extrac_features process-370859 starts
extrac_features process-370859, 200 hole_batches(50) proceed
extrac_features process-370866, 400 hole_batches(50) proceed
extrac_features process-370857, 400 hole_batches(50) proceed
extrac_features process-370864, 400 hole_batches(50) proceed
extrac_features process-370863, 400 hole_batches(50) proceed
extrac_features process-370860, 400 hole_batches(50) proceed
extrac_features process-370861, 400 hole_batches(50) proceed
extrac_features process-370865, 400 hole_batches(50) proceed
extrac_features process-370859, 400 hole_batches(50) proceed
extrac_features process-370866, 600 hole_batches(50) proceed
extrac_features process-370864, 600 hole_batches(50) proceed
extrac_features process-370857, 600 hole_batches(50) proceed
extrac_features process-370863, 600 hole_batches(50) proceed
extrac_features process-370860, 600 hole_batches(50) proceed
extrac_features process-370865, 600 hole_batches(50) proceed
extrac_features process-370861, 600 hole_batches(50) proceed
extrac_features process-370866, 800 hole_batches(50) proceed
extrac_features process-370859, 600 hole_batches(50) proceed
extrac_features process-370860, 800 hole_batches(50) proceed
extrac_features process-370863, 800 hole_batches(50) proceed
extrac_features process-370857, 800 hole_batches(50) proceed
extrac_features process-370864, 800 hole_batches(50) proceed
extrac_features process-370865, 800 hole_batches(50) proceed
extrac_features process-370861, 800 hole_batches(50) proceed
extrac_features process-370860, 1000 hole_batches(50) proceed
extrac_features process-370866, 1000 hole_batches(50) proceed
extrac_features process-370863, 1000 hole_batches(50) proceed
extrac_features process-370857, 1000 hole_batches(50) proceed
extrac_features process-370864, 1000 hole_batches(50) proceed
extrac_features process-370859, 800 hole_batches(50) proceed
extrac_features process-370865, 1000 hole_batches(50) proceed
extrac_features process-370860, 1200 hole_batches(50) proceed
extrac_features process-370861, 1000 hole_batches(50) proceed
extrac_features process-370863, 1200 hole_batches(50) proceed
extrac_features process-370866, 1200 hole_batches(50) proceed
extrac_features process-370857, 1200 hole_batches(50) proceed
extrac_features process-370864, 1200 hole_batches(50) proceed
extrac_features process-370860, 1400 hole_batches(50) proceed
extrac_features process-370865, 1200 hole_batches(50) proceed
extrac_features process-370861, 1200 hole_batches(50) proceed
extrac_features process-370863, 1400 hole_batches(50) proceed
extrac_features process-370857, 1400 hole_batches(50) proceed
extrac_features process-370866, 1400 hole_batches(50) proceed
extrac_features process-370859, 1000 hole_batches(50) proceed
extrac_features process-370864, 1400 hole_batches(50) proceed
extrac_features process-370860, 1600 hole_batches(50) proceed
extrac_features process-370865, 1400 hole_batches(50) proceed
extrac_features process-370863, 1600 hole_batches(50) proceed
extrac_features process-370857, 1600 hole_batches(50) proceed
extrac_features process-370861, 1400 hole_batches(50) proceed
extrac_features process-370866, 1600 hole_batches(50) proceed
extrac_features process-370860, 1800 hole_batches(50) proceed
extrac_features process-370864, 1600 hole_batches(50) proceed
extrac_features process-370865, 1600 hole_batches(50) proceed
extrac_features process-370863, 1800 hole_batches(50) proceed
extrac_features process-370857, 1800 hole_batches(50) proceed
extrac_features process-370866, 1800 hole_batches(50) proceed
extrac_features process-370861, 1600 hole_batches(50) proceed
extrac_features process-370859, 1200 hole_batches(50) proceed
extrac_features process-370860, 2000 hole_batches(50) proceed
extrac_features process-370865, 1800 hole_batches(50) proceed
extrac_features process-370864, 1800 hole_batches(50) proceed
extrac_features process-370857, 2000 hole_batches(50) proceed
extrac_features process-370863, 2000 hole_batches(50) proceed
extrac_features process-370866, 2000 hole_batches(50) proceed
extrac_features process-370861, 1800 hole_batches(50) proceed
extrac_features process-370860, 2200 hole_batches(50) proceed
extrac_features process-370864, 2000 hole_batches(50) proceed
extrac_features process-370865, 2000 hole_batches(50) proceed
extrac_features process-370859, 1400 hole_batches(50) proceed
extrac_features process-370866, 2200 hole_batches(50) proceed
extrac_features process-370857, 2200 hole_batches(50) proceed
extrac_features process-370861, 2000 hole_batches(50) proceed
extrac_features process-370864, 2200 hole_batches(50) proceed
extrac_features process-370863, 2200 hole_batches(50) proceed
extrac_features process-370860, 2400 hole_batches(50) proceed
extrac_features process-370865, 2200 hole_batches(50) proceed
extrac_features process-370857, 2400 hole_batches(50) proceed
extrac_features process-370859, 1600 hole_batches(50) proceed
extrac_features process-370866, 2400 hole_batches(50) proceed
extrac_features process-370861, 2200 hole_batches(50) proceed
extrac_features process-370860, 2600 hole_batches(50) proceed
extrac_features process-370864, 2400 hole_batches(50) proceed
extrac_features process-370863, 2400 hole_batches(50) proceed
extrac_features process-370865, 2400 hole_batches(50) proceed
extrac_features process-370857, 2600 hole_batches(50) proceed
extrac_features process-370866, 2600 hole_batches(50) proceed
extrac_features process-370861, 2400 hole_batches(50) proceed
extrac_features process-370864, 2600 hole_batches(50) proceed
extrac_features process-370863, 2600 hole_batches(50) proceed
extrac_features process-370860, 2800 hole_batches(50) proceed
extrac_features process-370859, 1800 hole_batches(50) proceed
extrac_features process-370865, 2600 hole_batches(50) proceed
extrac_features process-370857, 2800 hole_batches(50) proceed
extrac_features process-370866, 2800 hole_batches(50) proceed
extrac_features process-370863, 2800 hole_batches(50) proceed
extrac_features process-370864, 2800 hole_batches(50) proceed
extrac_features process-370861, 2600 hole_batches(50) proceed
extrac_features process-370865, 2800 hole_batches(50) proceed
extrac_features process-370860, 3000 hole_batches(50) proceed
extrac_features process-370857, 3000 hole_batches(50) proceed
extrac_features process-370859, 2000 hole_batches(50) proceed
extrac_features process-370863, 3000 hole_batches(50) proceed
extrac_features process-370864, 3000 hole_batches(50) proceed
extrac_features process-370866, 3000 hole_batches(50) proceed
extrac_features process-370865, 3000 hole_batches(50) proceed
extrac_features process-370860, 3200 hole_batches(50) proceed
extrac_features process-370857, 3200 hole_batches(50) proceed
extrac_features process-370861, 2800 hole_batches(50) proceed
extrac_features process-370863, 3200 hole_batches(50) proceed
extrac_features process-370866, 3200 hole_batches(50) proceed
extrac_features process-370864, 3200 hole_batches(50) proceed
extrac_features process-370865, 3200 hole_batches(50) proceed
extrac_features process-370857, 3400 hole_batches(50) proceed
extrac_features process-370859, 2200 hole_batches(50) proceed
extrac_features process-370861, 3000 hole_batches(50) proceed
extrac_features process-370860, 3400 hole_batches(50) proceed
extrac_features process-370863, 3400 hole_batches(50) proceed
extrac_features process-370864, 3400 hole_batches(50) proceed
extrac_features process-370865, 3400 hole_batches(50) proceed
extrac_features process-370866, 3400 hole_batches(50) proceed
extrac_features process-370860, 3600 hole_batches(50) proceed
extrac_features process-370857, 3600 hole_batches(50) proceed
extrac_features process-370861, 3200 hole_batches(50) proceed
extrac_features process-370863, 3600 hole_batches(50) proceed
extrac_features process-370859, 2400 hole_batches(50) proceed
extrac_features process-370864, 3600 hole_batches(50) proceed
extrac_features process-370865, 3600 hole_batches(50) proceed
extrac_features process-370866, 3600 hole_batches(50) proceed
extrac_features process-370857, 3800 hole_batches(50) proceed
extrac_features process-370863, 3800 hole_batches(50) proceed
extrac_features process-370861, 3400 hole_batches(50) proceed
extrac_features process-370860, 3800 hole_batches(50) proceed
extrac_features process-370864, 3800 hole_batches(50) proceed
extrac_features process-370865, 3800 hole_batches(50) proceed
extrac_features process-370859, 2600 hole_batches(50) proceed
extrac_features process-370863, 4000 hole_batches(50) proceed
extrac_features process-370866, 3800 hole_batches(50) proceed
extrac_features process-370857, 4000 hole_batches(50) proceed
extrac_features process-370864, 4000 hole_batches(50) proceed
extrac_features process-370860, 4000 hole_batches(50) proceed
extrac_features process-370865, 4000 hole_batches(50) proceed
extrac_features process-370861, 3600 hole_batches(50) proceed
extrac_features process-370866, 4000 hole_batches(50) proceed
extrac_features process-370857, 4200 hole_batches(50) proceed
extrac_features process-370863, 4200 hole_batches(50) proceed
extrac_features process-370864, 4200 hole_batches(50) proceed
extrac_features process-370865, 4200 hole_batches(50) proceed
extrac_features process-370859, 2800 hole_batches(50) proceed
extrac_features process-370860, 4200 hole_batches(50) proceed
extrac_features process-370861, 3800 hole_batches(50) proceed
extrac_features process-370857, 4400 hole_batches(50) proceed
extrac_features process-370864, 4400 hole_batches(50) proceed
extrac_features process-370865, 4400 hole_batches(50) proceed
extrac_features process-370863, 4400 hole_batches(50) proceed
extrac_features process-370866, 4200 hole_batches(50) proceed
extrac_features process-370860, 4400 hole_batches(50) proceed
extrac_features process-370857, 4600 hole_batches(50) proceed
extrac_features process-370859, 3000 hole_batches(50) proceed
extrac_features process-370861, 4000 hole_batches(50) proceed
extrac_features process-370864, 4600 hole_batches(50) proceed
extrac_features process-370863, 4600 hole_batches(50) proceed
extrac_features process-370866, 4400 hole_batches(50) proceed
extrac_features process-370865, 4600 hole_batches(50) proceed
extrac_features process-370857, 4800 hole_batches(50) proceed
extrac_features process-370860, 4600 hole_batches(50) proceed
extrac_features process-370861, 4200 hole_batches(50) proceed
read_input process-370856 starts
cmd to view input: samtools view -@ 3 -h m64081.pbmm2.bam
read_input process-370856 ending, read 1794590 holes, with return_code-0
extrac_features process-370861 ending, proceed 4236 hole_batches(50)
extrac_features process-370864 ending, proceed 4794 hole_batches(50)
extrac_features process-370863 ending, proceed 4774 hole_batches(50)
extrac_features process-370857 ending, proceed 4900 hole_batches(50)
extrac_features process-370859 ending, proceed 3175 hole_batches(50)
extrac_features process-370865 ending, proceed 4763 hole_batches(50)
extrac_features process-370860 ending, proceed 4674 hole_batches(50)
extrac_features process-370866 ending, proceed 4576 hole_batches(50)
write_process-370872 started
write_process-370872 finished
[extract_features]costs 1367.2 seconds

Any help is much appreciated. Thanks.

Best regards, Zhongping Xu

PengNi commented 2 years ago

Hi @tiramisutes , thanks for your interest of our tool. Right now for ccsmeth version<=0.1.2, the input of ccsmeth align should be subreads.bam not hifi.bam.

We are also now trying use hifi.bam with kinetics as input and are now re-training our model. It will be available later.

Best, Peng

tiramisutes commented 2 years ago

Thanks. Usually, the size of subreads.bam is so big. Looking forward to the release of the new version with a re-training model using hifi.bam.

gaushi commented 2 years ago

@PengNi : Many thanks for developing this excellent tool! I am using ccsmeth v0.2.3. I was wondering if you have already implemented using hifi.bam with kinetics as input in this version (so in this case I can use hifi.bam rather than subreads.bam)

Thank you again, Best, Gautam