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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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No events data in fast5 #29

Closed lqsae closed 3 years ago

lqsae commented 4 years ago

I have convert multi-fast5 to single fast5 file, but it has the the error Error!!! No events data in /mnt/CCX/User/liuqingshan/methylation/deepsignal/00.data/115.single_fast5_reads/109/c006ef2c-7bf4-432a-9e21-d1bc399c3766.fast5 can you help me?

liuqianhn commented 4 years ago

Hi @lqsae , could you please show me the output of h5ls -r /mnt/CCX/User/liuqingshan/methylation/deepsignal/00.data/115.single_fast5_reads/109/c006ef2c-7bf4-432a-9e21-d1bc399c3766.fast5 (I assume this fast5 file is for a single read; otherwise, please use head -n 50 to show the first 50 lines.).

lqsae commented 4 years ago

Thank you for your reply ,i have show the output . h5ls -r /mnt/CCX/User/liuqingshan/methylation/deepsignal/00.data/115.single_fast5_reads/208/68b3db20-2afb-4c4c-b981-c18c44da18b0.fast5 / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_55878 Group /Raw/Reads/Read_55878/Signal Dataset {12552/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group

lqsae commented 4 years ago

Thank you for your reply ,i have show the output . h5ls -r /mnt/CCX/User/liuqingshan/methylation/deepsignal/00.data/115.single_fast5_reads/208/68b3db20-2afb-4c4c-b981-c18c44da18b0.fast5 / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_55878 Group /Raw/Reads/Read_55878/Signal Dataset {12552/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group

刘青山

邮箱：18637315793@163.com |

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On 12/18/2019 22:22, liuqianhn wrote:

Hi @lqsae , could you please show me the output of h5ls -r /mnt/CCX/User/liuqingshan/methylation/deepsignal/00.data/115.single_fast5_reads/109/c006ef2c-7bf4-432a-9e21-d1bc399c3766.fast5 (I assume this fast5 file is for a single read; otherwise, please use head -n 50 to show the first 50 lines.).

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liuqianhn commented 4 years ago

Hi @lqsae , from your output, I do not find Event or Move in the fast5 file, and this is why this fast5 file has an issue. But it is normal if you have thousands of fast5 files and only tens of them have some issues in fast5.

lqsae commented 4 years ago

tank you very much , i have got it。

刘青山

18637315793@163.com | 签名由网易邮箱大师定制 On 12/18/2019 23:42，liuqianhnnotifications@github.com wrote：

Hi @lqsae , from your output, I do not find Event or Move in the fast5 file, and this is why this fast5 file has an issue. But it is normal if you have thousands of fast5 files and only tens of them have some issues in fast5.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

lqsae commented 4 years ago

I have run the program, but my result is empy。 I find that all my fast5 files don't contain move or evnet ,how can i solve the problem ?

liuqianhn commented 4 years ago

@lqsae , you can try albacore with the parameter of "--output_format fast5,fastq" and usually, event will be output.

lqsae commented 4 years ago

Hi ! the fast5 files contain evnet, but it stiil "Error!!! No events data in /mnt/CCX/User/liuqingshan/basecall/115/workspace/pass/0/48bc46de-0d8d-4800-8239-862fadcd082a.fast5"

h5ls -r /mnt/CCX/User/liuqingshan/basecall/115/workspace/pass/0/48bc46de-0d8d-4800-8239-862fadcd082a.fast5 / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Basecall_1D_001 Group /Analyses/Basecall_1D_001/BaseCalled_template Group /Analyses/Basecall_1D_001/BaseCalled_template/Events Dataset {4798} /Analyses/Basecall_1D_001/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_001/Configuration Group /Analyses/Basecall_1D_001/Configuration/basecall_1d Group /Analyses/Basecall_1D_001/Summary Group /Analyses/Basecall_1D_001/Summary/basecall_1d_template Group /Analyses/Calibration_Strand_Detection_000 Group /Analyses/Calibration_Strand_Detection_000/Configuration Group /Analyses/Calibration_Strand_Detection_000/Configuration/calib_detector Group /Analyses/Calibration_Strand_Detection_000/Summary Group /Analyses/Calibration_Strand_Detection_000/Summary/calibration_strand_template Group /Analyses/RawGenomeCorrected_000 Group /Analyses/RawGenomeCorrected_000/BaseCalled_template Group /Analyses/RawGenomeCorrected_000/BaseCalled_template/Alignment Group /Analyses/RawGenomeCorrected_000/BaseCalled_template/Events Dataset {1922} /Analyses/RawGenomeCorrected_001 Group /Analyses/RawGenomeCorrected_001/BaseCalled_template Group /Analyses/RawGenomeCorrected_001/BaseCalled_template/Alignment Group /Analyses/RawGenomeCorrected_001/BaseCalled_template/Events Dataset {2476} /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /Analyses/Segmentation_001 Group /Analyses/Segmentation_001/Configuration Group /Analyses/Segmentation_001/Configuration/stall_removal Group /Analyses/Segmentation_001/Summary Group

liuqianhn commented 4 years ago

Hi @lqsae , by default, the event is under Basecall_1D_000, while your event is under Basecall_1D_001. You might use --basecall_1d Basecall_1D_001 to set the event path for your fast5 file.

lqsae commented 4 years ago

tank you

liu2005678 commented 4 years ago

Hi, Dear @liuqianhn , you mentioned that either " Event or Move in the fast5 file" is acceptable for Deepmod, however, in my case, it continuously complained thing like "Error!!! No events data in ./44d5ad5e-3937-40c3-9411-eb93a0d3a148.fast5" . (guppy_basecaller version 3.4.5+fb1fbfb was used for basecalling and single fast5 was generate with ont_fast5_api, no "Event" tag). A command line using " h5ls -r 44d5ad5e-3937-40c3-9411-eb93a0d3a148.fast5" showed that it has the "Move" tag, as follows： / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/BaseCalled_template/Move Dataset {36010} /Analyses/Basecall_1D_000/BaseCalled_template/Trace Dataset {36010, 8} /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Basecall_1D_001 Group /Analyses/Basecall_1D_001/BaseCalled_template Group /Analyses/Basecall_1D_001/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_001/BaseCalled_template/Move Dataset {36010} /Analyses/Basecall_1D_001/BaseCalled_template/Trace Dataset {36010, 8} /Analyses/Basecall_1D_001/Summary Group /Analyses/Basecall_1D_001/Summary/basecall_1d_template Group /Analyses/RawGenomeCorrected_000 Group /Analyses/RawGenomeCorrected_000/BaseCalled_template Group /Analyses/RawGenomeCorrected_000/BaseCalled_template/Alignment Group /Analyses/RawGenomeCorrected_000/BaseCalled_template/Events Dataset {14780} /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /Analyses/Segmentation_001 Group /Analyses/Segmentation_001/Summary Group /Analyses/Segmentation_001/Summary/segmentation Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_696 Group /Raw/Reads/Read_696/Signal Dataset {144829/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group

should my datasets suitable for Deepmod, how to add the events. please!

liuqianhn commented 4 years ago

@lqsae , I guess you might not change the setting of --move which will use move table. By default, the value of --move is false, indicating event table is used. Could you please share the commands and this single fast5 file if you have set --move?

liu2005678 commented 4 years ago

there is no "--move" options in guppy_basecaller. the command I used is

guppy_basecaller -i /media/logen/PanD/Data/ -r -s /media/logen/PanE/aba_barcoded/ -x cuda:0 -c dna_r9.4.1_450bps_hac.cfg --num_callers 1 --gpu_runners_per_device 8 --chunks_per_runner 160 --fast5_out --barcode_kits SQK-RBK004 --trim_barcodes

And I checked the dna_r9.4.1_450bps_hac.cfg, it writes:

Basic configuration file for ONT Guppy basecaller software.

Compatibility

compatible_flowcells = FLO-FLG001,FLO-MIN106 compatible_kits = SQK-CAS109,SQK-DCS108,SQK-DCS109,SQK-LRK001,SQK-LSK108,SQK-LSK109,SQK-LSK109-XL,SQK-LWP001,SQK-PCS108,SQK-PCS109,SQK-PRC109,SQK-PSK004,SQK-RAD002,SQK-RAD003,SQK-RAD004,SQK-RAS201,SQK-RLI001,VSK-VBK001,VSK-VSK001,VSK-VSK002 compatible_kits_with_barcoding = SQK-16S024,SQK-PCB109,SQK-RBK001,SQK-RBK004,SQK-RLB001,SQK-LWB001,SQK-PBK004,SQK-RAB201,SQK-RAB204,SQK-RPB004,VSK-VMK001,VSK-VMK002

Data trimming.

trim_strategy = dna trim_threshold = 2.5 trim_min_events = 3

Basecalling.

model_file = template_r9.4.1_450bps_hac.jsn chunk_size = 1000 gpu_runners_per_device = 4 chunks_per_runner = 512 chunks_per_caller = 10000 overlap = 50 qscore_offset = 0.284 qscore_scale = 0.884 builtin_scripts = 1

Calibration strand detection

calib_reference = lambda_3.6kb.fasta calib_min_sequence_length = 3000 calib_max_sequence_length = 3800 calib_min_coverage = 0.6

Output.

records_per_fastq = 4000 min_qscore = 7.0

Telemetry

ping_url = https://ping.oxfordnanoportal.com/basecall ping_segment_duration = 60

The single fast5 file was used with multi_to_single_fast5, only -i -s -t -r options were set. a fast5 file was attached. with gzipped 0ae47c9f-cb82-4312-ab12-cc884b39e1a0.fast5.gz

liuqianhn commented 4 years ago

Hi @lqsae , I was talking about --move setting in DeepMod.

liu2005678 commented 4 years ago

much thanks

liu2005678 commented 4 years ago

By the way, some of my reads could not find channels by Deepmod, h5ls -r shows that: /read_d5df4431-8315-4983-835a-61c4d54c4d0a Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000 Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000/BaseCalled_template Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000/BaseCalled_template/Move Dataset {8386} /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000/BaseCalled_template/Trace Dataset {8386, 8} /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000/Summary Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Segmentation_000 Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Segmentation_000/Summary Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Analyses/Segmentation_000/Summary/segmentation Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Raw Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/Raw/Signal Dataset {16861/Inf} /read_d5df4431-8315-4983-835a-61c4d54c4d0a/channel_id Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/context_tags Group /read_d5df4431-8315-4983-835a-61c4d54c4d0a/tracking_id Group

How do I change these reads to be recognizable.

liu2005678 commented 4 years ago

solved by using h5copy， thanks。

lemonsky123 commented 4 years ago

solved by using h5copy， thanks。

Hi, @liu2005678 , I also met the same error, some of my reads could not find channels by Deepmod. Could you please show me the commands you used with h5copy? Thanks so much! Best.

liu2005678 commented 4 years ago

h5copy provided by the hdf5 group seem to be less efficiency. I made it by Python h5py API.
The scripts used:

import pandas as pd
import re import h5py

reads_info = pd.read_csv('E:/folder/sequencing_summary.txt', sep='\t') # read in the sequencing summary, as each fast5 had different reads ids. the read_d5df4431-8315-...

b=re.compile('_|.') d=[] filename=[] read_id=[] for i in reads_info['read_id']: read_id.append(i) for i in reads_info['filename']: filename.append(i) c=b.split(i) d.append(c[2])

for i in range(len(reads_info)): file_path='F:/fast6/'+ reads_info['filename'][i] #the fast5 read in file_write='d:\PF427\'+reads_info['filename'][i] # the fast5 to be written

print(file_path)

f2=h5py.File(file_path,'r')
analysis="read_"+read_id[i] + "/Analyses"
raw="read_"+read_id[i] + "/Raw/Signal"
raw2="/Raw/Reads/Read_"+d[i]
channel_id="read_"+read_id[i] +"/channel_id"
context_tags="read_"+read_id[i] +"/context_tags"
tracking_id="read_"+read_id[i] +"/tracking_id"
f3=h5py.File(file_write,'w')
f2.copy(analysis, f3)
grp1=f3.create_group(raw2)
grp2=f3.create_group("/UniqueGlobalKey")
f2.copy(raw,grp1)
f2.copy(channel_id,grp2)
f2.copy(context_tags,grp2)
f2.copy(tracking_id,grp2)
f2.close()
f3.close()
lemonsky123 commented 4 years ago

h5copy provided by the hdf5 group seem to be less efficiency. I made it by Python h5py API. The scripts used:

import pandas as pd import re import h5py

reads_info = pd.read_csv('E:/folder/sequencing_summary.txt', sep='\t') # read in the sequencing summary, as each fast5 had different reads ids. the read_d5df4431-8315-...

b=re.compile('_|.') d=[] filename=[] read_id=[] for i in reads_info['read_id']: read_id.append(i) for i in reads_info['filename']: filename.append(i) c=b.split(i) d.append(c[2])

for i in range(len(reads_info)): file_path='F:/fast6/'+ reads_info['filename'][i] #the fast5 read in file_write='d:\PF427\'+reads_info['filename'][i] # the fast5 to be written

print(file_path)

f2=h5py.File(filepath,'r') analysis="read"+readid[i] + "/Analyses" raw="read"+readid[i] + "/Raw/Signal" raw2="/Raw/Reads/Read"+d[i] channelid="read"+read_id[i] +"/channel_id" contexttags="read"+read_id[i] +"/context_tags" trackingid="read"+read_id[i] +"/tracking_id" f3=h5py.File(file_write,'w') f2.copy(analysis, f3) grp1=f3.create_group(raw2) grp2=f3.create_group("/UniqueGlobalKey") f2.copy(raw,grp1) f2.copy(channel_id,grp2) f2.copy(context_tags,grp2) f2.copy(tracking_id,grp2) f2.close() f3.close()

Thanks very much! Best.

liu2005678 commented 4 years ago

commands of h5copy....

h5copy -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/Analyses" -d "/Analyses"

h5copy -p -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/Raw/Signal" -d "/Raw/Reads/Read_1/Signal"

h5copy -p -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/channel_id" -d "/UniqueGlobalKey/channel_id"

h5copy -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/context_tags" -d "/UniqueGlobalKey/context_tags"

h5copy -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/tracking_id" -d "/UniqueGlobalKey/tracking_id"

h5copy -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/Analyses" -d "/Analyses" h5copy -p -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/Raw/Signal" -d "/Raw/Reads/Read_2/Signal" h5copy -p -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/channel_id" -d "/UniqueGlobalKey/channel_id" h5copy -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/context_tags" -d "/UniqueGlobalKey/context_tags" h5copy -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/tracking_id" -d "/UniqueGlobalKey/tracking_id"

lemonsky123 commented 4 years ago

commands of h5copy....

h5copy -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/Analyses" -d "/Analyses"

h5copy -p -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/Raw/Signal" -d "/Raw/Reads/Read_1/Signal"

h5copy -p -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/channel_id" -d "/UniqueGlobalKey/channel_id"

h5copy -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/context_tags" -d "/UniqueGlobalKey/context_tags"

h5copy -i "FAN03738_2139a5cc_0.fast5" -o "2_FAN03738_2139a5cc_0.fast5" -s "/read_d33822ee-1daf-4ff4-bcf4-a2e6881479f1/tracking_id" -d "/UniqueGlobalKey/tracking_id"

h5copy -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/Analyses" -d "/Analyses" h5copy -p -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/Raw/Signal" -d "/Raw/Reads/Read_2/Signal" h5copy -p -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/channel_id" -d "/UniqueGlobalKey/channel_id" h5copy -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/context_tags" -d "/UniqueGlobalKey/context_tags" h5copy -i "FAN03738_2139a5cc_1.fast5" -o "2_FAN03738_2139a5cc_1.fast5" -s "/read_37c95b46-28ce-4d46-8f29-c49a1620db44/tracking_id" -d "/UniqueGlobalKey/tracking_id"

Got it. Thanks! Best.

skerker commented 4 years ago

I have a similar problem with events data being in the wrong place for DeepMod to find it. Is h5copy the best solution, or is it possible to redo the basecalling with guppy in a way that puts things in the right locations?

Here is an example of my fast5 file:

(base) -bash-4.1$ h5ls -r 3fe3dea6-8608-4cc2-ab42-2e5510043e23.fast5 / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_001 Group /Analyses/Basecall_1D_001/BaseCalled_template Group /Analyses/Basecall_1D_001/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_001/BaseCalled_template/Move Dataset {48977} /Analyses/Basecall_1D_001/BaseCalled_template/Trace Dataset {48977, 8} /Analyses/Basecall_1D_001/Summary Group /Analyses/Basecall_1D_001/Summary/basecall_1d_template Group /Analyses/RawGenomeCorrected_000 Group /Analyses/RawGenomeCorrected_000/BaseCalled_template Group /Analyses/RawGenomeCorrected_000/BaseCalled_template/Alignment Group /Analyses/RawGenomeCorrected_000/BaseCalled_template/Events Dataset {6749} /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_001 Group /Analyses/Segmentation_001/Summary Group /Analyses/Segmentation_001/Summary/segmentation Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_13987 Group /Raw/Reads/Read_13987/Signal Dataset {98157/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group

liuqianhn commented 4 years ago

@skerker I see you have both move table and fastq under /Analyses/Basecall_1D_001/BaseCalled_template/. You can use move data after you set --move 1. Please note that you also need to set --basecall_1d Basecall_1D_001 since the default value of basecall_1d is Basecall_1D_000.

skerker commented 4 years ago

Thank you!

I set --move and --basecall_1d Basecall_1D_001 and now it is running.

liuqianhn commented 4 years ago

@skerker Great. Please also note that the event data you hightlighted is generated by Nanoraw or Tombo rather than by basecaller and thus might be wrong for DeepMod.

skerker commented 4 years ago

OK thanks. Yes, I ran tombo resquiggle on this - which generated that events table, which I guess is the wrong thing for DeepMod.

But the move table is from my guppy basecaller run. So I think I'm OK for deepmod, using --move and --basecall_1d Basecall_1D_001?

Jerry-0591 commented 4 years ago

Basecall_1D_000 Hi, I have a question about Basecall_1D_000 and Basecall_1D_001, what is the difference between them? Should I do something to check the base-calling result in this two parts are right, otherwise DeepMod will meet some problems?

liuqianhn commented 4 years ago

The difference between Basecall_1D_000 and Basecall_1D_001: sometimes, you might baseball the data twice, and both are in the fast5 files, and they are list with different Basecall_1D ids. You need to check your several fast5 files to see which one you have. Usually, it is Basecall_1D_000.

liuqianhn commented 3 years ago

Closed due to no recent response. Feel free to reopen it if you need more help.