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Error!!! No Channel Info in /users/PAE57595_pass_barcode01_83605eaf_16.fast5 #39
It seems that there is no channel info in your fast5 files. Please show the output of "h5ls -r /users/PAE57595_pass_barcode01_83605eaf_16.fast5 | head -n 50" so that I can comment more.
您的fast5文件中似乎没有频道信息。请显示“ h5ls -r /users/PAE57595_pass_barcode01_83605eaf_16.fast5 | head -n 50”的输出，以便我进一步评论。
Thank you, teacher. My first 50 lines are as follows. How should I deal with the original FAST5 file?
/ Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Basecall_1D_000 Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Basecall_1D_000/BaseCalled_template Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR}
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Basecall_1D_000/Summary Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Segmentation_000 Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Segmentation_000/Summary Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Analyses/Segmentation_000/Summary/segmentation Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Raw Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/Raw/Signal Dataset {163018/Inf}
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/channel_id Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/context_tags Group
/read_001009ec-891e-4377-86d2-06ceab0cb2ad/tracking_id Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4 Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Basecall_1D_000 Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Basecall_1D_000/BaseCalled_template Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR}
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Basecall_1D_000/Summary Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Segmentation_000 Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Segmentation_000/Summary Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Analyses/Segmentation_000/Summary/segmentation Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Raw Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/Raw/Signal Dataset {165995/Inf}
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/channel_id Group
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/context_tags Group, same as /read_001009ec-891e-4377-86d2-06ceab0cb2ad/context_tags
/read_0029e9f8-d867-4b18-a727-481ada57a2f4/tracking_id Group, same as /read_001009ec-891e-4377-86d2-06ceab0cb2ad/tracking_id
/read_002b4830-62da-4e62-a54a-4ae609d95007 Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Basecall_1D_000 Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Basecall_1D_000/BaseCalled_template Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR}
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Basecall_1D_000/Summary Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Segmentation_000 Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Segmentation_000/Summary Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Analyses/Segmentation_000/Summary/segmentation Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Raw Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/Raw/Signal Dataset {61491/Inf}
/read_002b4830-62da-4e62-a54a-4ae609d95007/channel_id Group
/read_002b4830-62da-4e62-a54a-4ae609d95007/context_tags Group, same as /read_001009ec-891e-4377-86d2-06ceab0cb2ad/context_tags
/read_002b4830-62da-4e62-a54a-4ae609d95007/tracking_id Group, same as /read_001009ec-891e-4377-86d2-06ceab0cb2ad/tracking_id
/read_00435e94-11d6-40b5-b5e2-561c9f9ad45e Group
/read_00435e94-11d6-40b5-b5e2-561c9f9ad45e/Analyses Group
/read_00435e94-11d6-40b5-b5e2-561c9f9ad45e/Analyses/Basecall_1D_000 Group
/read_00435e94-11d6-40b5-b5e2-561c9f9ad45e/Analyses/Basecall_1D_000/BaseCalled_template Group
@chenchen-eng Your fast5 files have multi-fast5 format, and the tool is not supported yet. You can use ont_fast5_api to convert them to single-fast5 format before using the tools. We are working on the improvement of the tool including multi-fast5 format supporting, but the improvement is not available in a short time.
teacher，How should this error be resolved?Error!!! No Fastq data in /users/xulab/lida/m6a/01_PH-1/20200810_1005_4G_PAE88034_798dbc59/output/71/8016b946-83a0-4db4-bc82-780698a2be82.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/Fastq Dataset {SCALAR}
/Analyses/Basecall_1D_001/BaseCalled_template/ModBaseProbs Dataset {6886, 6}
/Analyses/Basecall_1D_001/BaseCalled_template/Move Dataset {35312}
/Analyses/Basecall_1D_001/BaseCalled_template/Trace Dataset {35312, 8}
/Analyses/Basecall_1D_001/Summary Group
/Analyses/Basecall_1D_001/Summary/basecall_1d_template Group
/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_9383 Group
/Raw/Reads/Read_9383/Signal Dataset {72404/Inf}
/UniqueGlobalKey Group
/UniqueGlobalKey/channel_id Group
/UniqueGlobalKey/context_tags Group
/UniqueGlobalKey/tracking_id Group
no events data?teacher
You can find ont_fast5_API via the link I provided. I think, you already install and use it.
If there are errors such as No Fastq or no events, what you can do is:
Use h5ls -r to check the path in fasta5 files as you did. In fact, in your fast5 file, you have two basecalled branch: Basecall_1D_000 and Basecall_1D_001. You need to make sure that the path is correct to find fastq and event via --basecall_1d Basecall_1D_000 or --basecall_1d Basecall_1D_001. Here, --basecall_1d Basecall_1D_000 is the default option. In your example fast5 file, the default option does not work since your Basecall_1D_000 in this file does not have complete results.
If no events happens, you also need to use h5ls -r to check the path in fasta5 files as you did. In your example file, it seems that you have move table rather than events, thus, you need to --move True to tell the tool to find move table rather than events table.
In short, adding --basecall_1d Basecall_1D_000 --move True to your running command should solve the issue you have.
Please note that the available well-trained model is not updated, and I have worked on the improvement. But the improvement cannot be available in a short time.
Activity
liuqianhn commentedon Sep 4, 2020
It seems that there is no channel info in your fast5 files. Please show the output of "h5ls -r /users/PAE57595_pass_barcode01_83605eaf_16.fast5 | head -n 50" so that I can comment more.
chenchen-eng commentedon Sep 4, 2020
liuqianhn commentedon Sep 4, 2020
@chenchen-eng Your fast5 files have multi-fast5 format, and the tool is not supported yet. You can use ont_fast5_api to convert them to single-fast5 format before using the tools. We are working on the improvement of the tool including multi-fast5 format supporting, but the improvement is not available in a short time.
chenchen-eng commentedon Sep 5, 2020
Thank you, can We use ont_fast5_API?The teacher?Mine is a fungus sample. Can your model be used directly?
chenchen-eng commentedon Sep 5, 2020
teacher，How should this error be resolved?Error!!! No Fastq data in /users/xulab/lida/m6a/01_PH-1/20200810_1005_4G_PAE88034_798dbc59/output/71/8016b946-83a0-4db4-bc82-780698a2be82.fast5
chenchen-eng commentedon Sep 5, 2020
/ 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/Fastq Dataset {SCALAR}
/Analyses/Basecall_1D_001/BaseCalled_template/ModBaseProbs Dataset {6886, 6}
/Analyses/Basecall_1D_001/BaseCalled_template/Move Dataset {35312}
/Analyses/Basecall_1D_001/BaseCalled_template/Trace Dataset {35312, 8}
/Analyses/Basecall_1D_001/Summary Group
/Analyses/Basecall_1D_001/Summary/basecall_1d_template Group
/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_9383 Group
/Raw/Reads/Read_9383/Signal Dataset {72404/Inf}
/UniqueGlobalKey Group
/UniqueGlobalKey/channel_id Group
/UniqueGlobalKey/context_tags Group
/UniqueGlobalKey/tracking_id Group
no events data?teacher
liuqianhn commentedon Sep 5, 2020
No Fastqorno events, what you can do is:Use
h5ls -rto check the path in fasta5 files as you did. In fact, in your fast5 file, you have two basecalled branch:Basecall_1D_000andBasecall_1D_001. You need to make sure that the path is correct to find fastq and event via--basecall_1d Basecall_1D_000or--basecall_1d Basecall_1D_001. Here,--basecall_1d Basecall_1D_000is the default option. In your example fast5 file, the default option does not work since yourBasecall_1D_000in this file does not have complete results.no eventshappens, you also need to useh5ls -rto check the path in fasta5 files as you did. In your example file, it seems that you havemovetable rather thanevents, thus, you need to--move Trueto tell the tool to findmovetable rather thaneventstable.In short, adding
--basecall_1d Basecall_1D_000 --move Trueto your running command should solve the issue you have.Please note that the available well-trained model is not updated, and I have worked on the improvement. But the improvement cannot be available in a short time.