Open zmy24 opened 2 years ago
@zmy24 Thank you for using DeepMod.
Hi @liuqianhn I got a similar error in DeepMod when i have re-basecalled the single fast5 file. / 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_001 Group /Analyses/Basecall_1D_001/BaseCalled_template Group /Analyses/Basecall_1D_001/BaseCalled_template/Events Dataset {1754} /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 {1200} /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_8036 Group /Raw/Reads/Read_8036/Signal Dataset {8911/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group
Meanwhile, I set the --basecall_1d
as Basecall_1D_001. But it still showed as "No events data 3596".
Can you help me? Thanks a lot!
@Bin-Ma Could you please share this fast5 file and the command you use? Please also kindly share the log output if you have. Thanks.
@Bin-Ma Could you please share this fast5 file and the command you use? Please also kindly share the log output if you have. Thanks.
@liuqianhn Thanks for your reply! I have uploaded the test data and log file. By the way, The command was generated as follow.
python ~/software/DeepMod/bin/DeepMod.py detect --wrkBase ../barcode_fast5/single/1/output/workspace/pass/test/ --Ref ../fna/barcode01.fna --outFolder ./barcode_test --Base A --modfile ~/software/DeepMod/train_deepmod/rnn_sinmodC_P100wd21_f7ne1u0_4/mod_train_sinmodC_P100wd21_f3ne1u0 --FileID test1 --threads 80 --basecall_1d Basecall_1D_001 > deepmod_test.log 2>&1
@Bin-Ma I checked the issue and your command.
--Base
, while the trained model is for C.
I'm trying to call DNA modifications by using Deepmod. First, I used Guppy for basecalling. And then, run Deepmod to call DNA modifications. But it has the error 'Cannot open fast5 or other errors: '. This is the output of h5ls -r of my fast5 file: / Group /Analyses Group /Analyses/Barcoding_000 Group /Analyses/Barcoding_000/Barcoding Group /Analyses/Barcoding_000/Barcoding/Aligns Dataset {756} /Analyses/Barcoding_000/Barcoding/Fastq Dataset {SCALAR} /Analyses/Barcoding_000/Configuration Group /Analyses/Barcoding_000/Configuration/aggregator Group /Analyses/Barcoding_000/Configuration/barcoding Group /Analyses/Barcoding_000/Configuration/basecall_1d Group /Analyses/Barcoding_000/Configuration/basecall_2d Group /Analyses/Barcoding_000/Configuration/calibration_strand Group /Analyses/Barcoding_000/Configuration/components Group /Analyses/Barcoding_000/Configuration/general Group /Analyses/Barcoding_000/Configuration/hairpin_align Group /Analyses/Barcoding_000/Configuration/post_processing.3000Hz Group /Analyses/Barcoding_000/Configuration/split_hairpin Group /Analyses/Barcoding_000/Log Dataset {SCALAR} /Analyses/Barcoding_000/Summary Group /Analyses/Barcoding_000/Summary/barcoding Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_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 {75012} /Analyses/Basecall_1D_001/BaseCalled_template/StateData Dataset {75012, 40} /Analyses/Basecall_1D_001/BaseCalled_template/Trace Dataset {75012, 8} /Analyses/Basecall_1D_001/Summary Group /Analyses/Basecall_1D_001/Summary/basecall_1d_template Group /Analyses/Basecall_2D_000 Group /Analyses/Basecall_2D_000/BaseCalled_2D Group /Analyses/Basecall_2D_000/BaseCalled_2D/Alignment Dataset {5654} /Analyses/Basecall_2D_000/BaseCalled_2D/Fastq Dataset {SCALAR} /Analyses/Basecall_2D_000/Configuration Group /Analyses/Basecall_2D_000/Configuration/aggregator Group /Analyses/Basecall_2D_000/Configuration/basecall_1d Group /Analyses/Basecall_2D_000/Configuration/basecall_2d Group /Analyses/Basecall_2D_000/Configuration/calibration_strand Group /Analyses/Basecall_2D_000/Configuration/components Group /Analyses/Basecall_2D_000/Configuration/event_detection Group /Analyses/Basecall_2D_000/Configuration/general Group /Analyses/Basecall_2D_000/Configuration/hairpin_align Group /Analyses/Basecall_2D_000/Configuration/post_processing Group /Analyses/Basecall_2D_000/Configuration/post_processing.4000Hz Group /Analyses/Basecall_2D_000/Configuration/split_hairpin Group /Analyses/Basecall_2D_000/HairpinAlign Group /Analyses/Basecall_2D_000/HairpinAlign/Alignment Dataset {4053} /Analyses/Basecall_2D_000/Log Dataset {SCALAR} /Analyses/Basecall_2D_000/Summary Group /Analyses/Basecall_2D_000/Summary/basecall_2d Group /Analyses/Basecall_2D_000/Summary/hairpin_align Group /Analyses/Basecall_2D_000/Summary/post_process_complement Group /Analyses/Basecall_2D_000/Summary/post_process_template Group /Analyses/Calibration_Strand_000 Group /Analyses/Calibration_Strand_000/Configuration Group /Analyses/Calibration_Strand_000/Configuration/aggregator Group /Analyses/Calibration_Strand_000/Configuration/basecall_1d Group /Analyses/Calibration_Strand_000/Configuration/basecall_2d Group /Analyses/Calibration_Strand_000/Configuration/calibration_strand Group /Analyses/Calibration_Strand_000/Configuration/components Group /Analyses/Calibration_Strand_000/Configuration/general Group /Analyses/Calibration_Strand_000/Configuration/genome_mapping Group /Analyses/Calibration_Strand_000/Configuration/hairpin_align Group /Analyses/Calibration_Strand_000/Configuration/post_processing.3000Hz Group /Analyses/Calibration_Strand_000/Configuration/split_hairpin Group /Analyses/Calibration_Strand_000/Log Dataset {SCALAR} /Analyses/Calibration_Strand_000/Summary Group /Analyses/EventDetection_000 Group /Analyses/EventDetection_000/Configuration Group /Analyses/EventDetection_000/Configuration/aggregator Group /Analyses/EventDetection_000/Configuration/basecall_1d Group /Analyses/EventDetection_000/Configuration/basecall_2d Group /Analyses/EventDetection_000/Configuration/calibration_strand Group /Analyses/EventDetection_000/Configuration/components Group /Analyses/EventDetection_000/Configuration/event_detection Group /Analyses/EventDetection_000/Configuration/general Group /Analyses/EventDetection_000/Configuration/hairpin_align Group /Analyses/EventDetection_000/Configuration/post_processing Group /Analyses/EventDetection_000/Configuration/post_processing.4000Hz Group /Analyses/EventDetection_000/Configuration/split_hairpin Group /Analyses/EventDetection_000/Log Dataset {SCALAR} /Analyses/EventDetection_000/Reads Group /Analyses/EventDetection_000/Reads/Read_10536 Group /Analyses/EventDetection_000/Reads/Read_10536/Events Dataset {9334} /Analyses/EventDetection_000/Summary Group /Analyses/EventDetection_000/Summary/event_detection Group /Analyses/Hairpin_Split_000 Group /Analyses/Hairpin_Split_000/Configuration Group /Analyses/Hairpin_Split_000/Configuration/aggregator Group /Analyses/Hairpin_Split_000/Configuration/basecall_1d Group /Analyses/Hairpin_Split_000/Configuration/basecall_2d Group /Analyses/Hairpin_Split_000/Configuration/calibration_strand Group /Analyses/Hairpin_Split_000/Configuration/components Group /Analyses/Hairpin_Split_000/Configuration/event_detection Group /Analyses/Hairpin_Split_000/Configuration/general Group /Analyses/Hairpin_Split_000/Configuration/hairpin_align Group /Analyses/Hairpin_Split_000/Configuration/post_processing Group /Analyses/Hairpin_Split_000/Configuration/post_processing.4000Hz Group /Analyses/Hairpin_Split_000/Configuration/split_hairpin Group /Analyses/Hairpin_Split_000/Log Dataset {SCALAR} /Analyses/Hairpin_Split_000/Summary Group /Analyses/Hairpin_Split_000/Summary/split_hairpin Group /Analyses/RawGenomeCorrected_000 Group /Analyses/RawGenomeCorrected_000/BaseCalled_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_10536 Group /Raw/Reads/Read_10536/Signal Dataset {390818/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group
And this is my code for Deepmod: python ./bin/DeepMod.py detect --wrkBase path_for_fast5 --Ref unidentified_spots_contigs.fasta --outFolder NB08 --Base C --modfile ./DeepMod/train_deepmod/rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0 --FileID NB08 --basecall_1d Basecall_1D_001 --threads 1 --move
Can you help me? Thanks a lot!