output files made by SquigglePull.py containing nothing

[liu-pinnng]

Hi,

Thank you for developing and maintaining this project!
I am trying to extract the raw signal using SquigglePull.py.
It seems to work, but the .tsv files were containing nothing.
Can you help me with this problem?
Thank you in advance.

Ping

[Psy-Fer]

Hello Ping,

Sure. Could you please tell me a few things?

Python version?
Single or multi fast5 files?
Command being used?
Operating system?

Thanks!

[liu-pinnng]

Hi,

Thank you for your quick reply.
Python version: Python 3.6.10
Single fast5 file
Command as python SquigglePull.py -r -p downloads/SquiggleKit/example/test.fast5/ > data6.tsv
Operating system: macOS 10.14.6

Ping

[Psy-Fer]

Thanks for that Ping.

Try chaning the command to just the top folder, rather than the individual file

python SquigglePull.py -r -p downloads/SquiggleKit/example/ > data6.tsv

The -p is meant to take a path as an argument. It then finds every fast5 file in that folder after that.

Also, when I asked if it was single or multi. I didn't mean "multiple files" or a "single file" I mean the format of the fast5 file itself. Does the file contain onle 1 read, or does it contain multiple reads. The latest sequencing runs will have multi-fast5 format, usually containing ~4000 reads per file.

[liu-pinnng]

Thanks for your kind comment.

I used this comment.
python SquigglePull.py -r -p downloads/SquiggleKit/example/ > data6.tsv
But still, nothing containing in the .tsv.
The data I used was downloaded from SquiggleKit.

The data I want to use is the multi-fast5 format.

[Psy-Fer]

Ahh, try adding the --multi flag

[liu-pinnng]

Still does not work.

[liu-pinnng]

I worked in the following command.
(envs) PINGdeMacBook-Pro:SquiggleKit pingliu$ python SquigglePull.py -r -p downloads/SquiggleKit/example/ --multi > data.tsv

[liu-pinnng]

It seems to work by adding ~/ in the front of the path.
However, when I tried to use my own .fast5 with --multi, the key error showed as follow:
KeyError: 'Unable to open object (component not found)'
extract_fast5():failed to read readID: UniqueGlobalKey(envs) PINGdeMacBook-Pro:SquiggleKit pingliu$

[Psy-Fer]

Ahh. That is weird.

Let me do some tests to se if I can figure it out.

[TTT16]

Hi, Has this issue got fixed? I ran into the same problem. Please help to provide the solution. Thank you!

[Psy-Fer]

I have narrowed this down to be an issue with various fast5 versions. and they way the files are written by ONT. Given slow5 and pod5 are the dominant file formats with working converters, I don't plan on fixing things like this with fast5 as the development time is not worth it.

SquigglePull is not really needed anymore, as you should be able to use the raw files directly with the downstream tools. The tsv intermediate format was an early prototype of what turned into the SLOW5 file format.

James

[TTT16]

Hi Jame, My own data was from GridIOn, Nanopore Directed RNA seq. The output files were fast5 and fastq. The fast5 files are multi-read files. We tried the SquigglePlot directly on those *.fast5, but the command did not work. In case of my output files like that, would you pls recommend the Squiggle Plot command? Thank you, Trinh

…

On Thu, Mar 21, 2024 at 3:02 AM James Ferguson ***@***.***> wrote: I have narrowed this down to be an issue with various fast5 versions. and they way the files are written by ONT. Given slow5 and pod5 are the dominant file formats with working converters, I don't plan on fixing things like this with fast5 as the development time is not worth it. SquigglePull is not really needed anymore, as you should be able to use the raw files directly with the downstream tools. The tsv intermediate format was an early prototype of what turned into the SLOW5 file format. James — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALAPWNT2TQAH6AEUBWQOPPDYZKHXZAVCNFSM4U5SQ4G2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMBRGE2DSMJWGA2A> . You are receiving this because you commented.Message ID: ***@***.***>