No events data in fast5

[fire-activate]

My instructions are /home/qiulimei/softwore/DeepMod/bin/DeepMod.py detect --Ref /home/qiulimei/nanopolish/reference.fasta --modfile /home/qiulimei/softwore/DeepMod/train_deepmod/rnn_conmodA_P100wd21_f7ne1u0_4/mod_train_conmodA_P100wd21_f3ne1u0 --Base A --wrkBase /home/qiulimei/nanopolish/output/workspace/pass --outFolder /home/qiulimei/nanopolish/result
But there is： Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/2d938cbc-7e74-43fb-98c4-db98ebd4b1fc.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/71a14234-8cf3-425c-8195-75c90cd156f6.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/3bddd188-3d9a-4e58-ac9f-473769f4ee90.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/50fbbdbc-6bbe-4c7d-ab2a-d9dcc96daf0d.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/d7134f4a-063c-4f58-b30c-194c5100fc51.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/27a978e1-ef10-4ab2-87d7-a525b220b749.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/29b03e41-2a10-4cb4-a094-1f9f0db37a81.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/7c9338db-5059-4b23-a32b-e3b7aef93154.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/b0b3ecd8-0e41-46b1-87e9-e98487a0e17a.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/354f8a1c-5915-4940-9f02-24e42d593a7e.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/38ae0330-75ee-4747-b8f8-cfb0c2a9c615.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/0590a065-ab0e-40c5-9562-0f07cfe83ce3.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/c921a7d4-d9e1-4acf-b508-03ca71864ca8.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/bd4e8d11-0d3a-43bc-bec7-3c75d2c19fc5.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/d6e5e65e-5122-45c0-8cdb-69244367c612.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/09148b02-9329-4c1a-8169-94a3d4bf717a.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/95f1e3d8-256a-4e9d-a536-094306fedc44.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/28fe0b1d-2744-4145-8814-83107af6050d.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/3025d690-58d8-4c1e-bcb1-176fcc4ba170.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/3ba3d195-2a09-46c6-9a09-26844f953b7e.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/a9c5c809-5183-43d9-b94d-d9bc35205e3f.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/0b7e0f36-06f4-4ea9-8c37-fe94e9b5be8b.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/fa29b6d8-4951-46f9-9b90-e44e89916252.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/89fd0ba5-dfcb-412f-892b-8f8786e19006.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/254a6a95-a610-4ed8-b95a-6527a237fc42.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/0ddce77b-3be8-441a-b0e7-1f654b486015.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/35db9fb2-def5-472b-ac57-0933f4333467.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/1597565a-35d7-43bb-a00b-871eb482865a.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/3d5d9b2f-4aab-412a-a951-2a8f7daf2f18.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/d6b44bf7-a750-4035-b15f-3f39909cedac.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/dc14e352-2793-4736-bc92-bb3e999e2508.fast5
Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/d7878d33-a0ac-4d70-bdab-c44b90a8cb46.fast5
.....
I checked one of the fast5 files and found that there was an event
/ Group
/Analyses Group
/Analyses/Basecall_1D_000 Group
/Analyses/Basecall_1D_000/BaseCalled_template Group
/Analyses/Basecall_1D_000/BaseCalled_template/Events Dataset {17342}
/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR}
/Analyses/Basecall_1D_000/Configuration Group
/Analyses/Basecall_1D_000/Configuration/basecall_1d Group
/Analyses/Basecall_1D_000/Summary Group
/Analyses/Basecall_1D_000/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/Segment_Linear_000 Group
/Analyses/Segment_Linear_000/Summary Group
/Analyses/Segment_Linear_000/Summary/split_hairpin Group
/Analyses/Segmentation_000 Group
/Analyses/Segmentation_000/Configuration Group
/Analyses/Segmentation_000/Configuration/stall_removal Group
/Analyses/Segmentation_000/Summary Group
/Analyses/Segmentation_000/Summary/segmentation Group
/Raw Group
/Raw/Reads Group
/Raw/Reads/Read_7524 Group
/Raw/Reads/Read_7524/Signal Dataset {87217/Inf}
/UniqueGlobalKey Group
/UniqueGlobalKey/channel_id Group
/UniqueGlobalKey/context_tags Group
/UniqueGlobalKey/tracking_id Group
I don't know what the problem is, can you answer it for me?I look forward to hearing from you

[liuqianhn]

@fire-activate It is because of the issue of h5py (the line with issue is

DeepMod/bin/DeepMod_scripts/myDetect.py

Line 157 in 9845295

events_data = sp_param['f5reader'][event_path].value

).
Please refer to DeepMod2 for the updated tool.

[fire-activate]

Do I just use deepmod2 to solve the problem?

@fire激活这是因为h5py的问题（与问题的行是

DeepMod/bin/DeepMod_scripts/myDetect.py

Line 157 in 9845295

events_data = sp_param['f5reader'][event_path].value

).
请参阅 DeepMod2 以获取更新后的工具。

Do I just use deepmod2 to solve the problem?

[fire]

Hi

[fire-activate]

Hi

HI

[liuqianhn]

@fire Please kindly create an issue in DeepMod2, since the developer of DeepMod2 might not check this issue.