slow5tools

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Error in slow5tools merge

2

Hi, I tried to use fast5toslow5 to convert the fast5 files to slow5 and then merge them into a single file. I am getting the following error during the merge...

lyj95618

Ensuring File Integrity and Accuracy in Processing Custom Genome blow5 Files

2

Hello, I apologise if this is not the right location to make this type of enquiry. I am completing my master's in diagnostics genomics and I have some concerns and...

KDalcin

Could not create read group in fast5 file

5

Dear slow5tools developers, When working with the following blow5 file: [https://github.com/Theo-Nelson/SMS-data/raw/main/HCV/HCV_IVT_004_ALIGNED_SIGNALS.blow5](https://github.com/Theo-Nelson/SMS-data/raw/main/HCV/HCV_IVT_004_ALIGNED_SIGNALS.blow5) I received the following error message: [list_all_items] Looking for '*low5' files in /content/HCV_IVT_004_ALIGNED_SIGNALS.blow5 [s2f_main] 1 files found - took...

Theo-Nelson

Bad fast5: Attribute Raw/tracked_scaling_scale

9

Hi I got the following error messages: Bad fast5: Attribute Raw/tracked_scaling_scale in /groups/chengrp/dRNAseq/157_-DEX_dRNAseq/157_-DEX/20231031_0244_MC-110944_FAQ79114_c4653c1d/fast5/FAQ79114_c4653c1d_d8ce327a_77.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate. Bad...

nickst85

sashajenner

Setting custom prefix is ignored during install

2

The supplied Makefile ignores the prefix variable set during configuration. ### Steps to reproduce: ``` wget "https://github.com/hasindu2008/slow5tools/releases/download/v1.2.0/slow5tools-v1.2.0-release.tar.gz" tar -xzf slow5tools-v1.2.0-release.tar.gz cd slow4tools-v1.2.0 ./configure --prefix=$HOME/.local # or any other directory make...

ForrestCKoch

Wrong stats in slow5tools get when --skip is used

1

For myself later: ``` nstall/slow5tools-v1.3.0/slow5tools index PGXXSX240470_reads_chr22.blow5 [get_main::WARNING] Will skip records that are not found [get_main] Fetched 4065 reads of 4096 [get_main] Fetched 4026 reads of 4096 [get_main] Fetched 3993...

hasindu2008

Implicit requirement in `split` that the column specified with `--demux-rid` must occur before `--demux-code`

1

Hi Hasindu, thanks for this super useful tool! I'm currently demultiplexing a large dataset and am supplying custom demultiplexing data. I noticed that when I have a tsv file where...

patbohn

slow5tools degrade (1.3.0) does not detect ULK kit?

5

For the following s/blow5 header made with blue-crab (0.1.2) , it does not seem that slow5tools degrade (1.3.0) recognizes the ULK kit. ```bash #slow5_version 0.2.0 #num_read_groups 1 @acquisition_id ca82937006c473b34e065122cf6a8ed73c55ce18 @acquisition_start_time...

jelber2