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jts / nanopolish

Signal-level algorithms for MinION data
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Error getting group name size #1089

Open gsukrit opened 1 year ago

gsukrit commented 1 year ago

Hi,

I was trying out the nanopolish index which consistently gave me the error as follows:

[readdb] indexing /DATA/BioLab/Sukriti/PF_FAS70460_IIT/ACD_pass_FAST5/barcode02/ error getting group name size

I had barcoded 3 samples in the run and the same command worked fine on barcode01 and barcode03.

I also tried converting the faast5 to slow5 as suggested by people in earlier issues without any luck.

Any help on the same will be appreciated.

Thanks, Sukriti

jts commented 1 year ago

Hm, if it worked on barcode01 and barcode 03 it might mean the fast5 for barcode02 is corrupted somehow. Perhaps try to identify which fast5 doesn't work?

hasindu2008 commented 1 year ago

@gsukrit when converting from fast5>blow5, it should print to the stderr which file gives this error getting group name size. If you put the log from slow5tools f2s, I can pinpoint which file it is. Once you remove that file, reindex with nanopolish and execute it works in most cases (unless more files are corrupted, for which you can repeat this process).

gsukrit commented 1 year ago

Hi,

Can you please let me know how to identify which of the fast5 is corrupted? I am using the fast5 directory of the reads classified under the "pass'' folder after the base calling.

Thanks, Sukriti

On Fri, Jun 16, 2023 at 8:44 PM Jared Simpson @.***> wrote:

Hm, if it worked on barcode01 and barcode 03 it might mean the fast5 for barcode02 is corrupted somehow. Perhaps try to identify which fast5 doesn't work?

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hasindu2008 commented 1 year ago

@gsukrit Could you do a slow5tools f2s fast5_directory -d slow5 and copy paste the log messages?