search

Psy-Fer / SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data
MIT License
120 stars 23 forks source link

output files made by SquigglePull.py containing nothing #43

Open liu-pinnng opened 3 years ago

liu-pinnng commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

Ahh, try adding the --multi flag

liu-pinnng commented 3 years ago

Still does not work.

liu-pinnng commented 3 years ago

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

liu-pinnng commented 3 years ago

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 commented 3 years ago

Ahh. That is weird.

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

TTT16 commented 3 months ago

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

Psy-Fer commented 3 months ago

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 commented 3 months ago

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 https://github.com/Psy-Fer/SquiggleKit/issues/43#issuecomment-2011491604, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAPWNT2TQAH6AEUBWQOPPDYZKHXZAVCNFSM4U5SQ4G2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMBRGE2DSMJWGA2A . You are receiving this because you commented.Message ID: @.***>