MotifSeq seg faulting at read_bait_model

[690645258]

Hi again,

I'm trying to run MotifSeq on my newly acquired SquigglePull data (thanks again for fixing that!) but I keep on getting the following error message:

Traceback (most recent call last): File "/home/user/tools/SquiggleKit/MotifSeq.py", line 520, in <module> main() File "/home/user/tools/SquiggleKit/MotifSeq.py", line 153, in main model, m_order, L = read_bait_model(args.model) File "/home/user/tools/SquiggleKit/MotifSeq.py", line 420, in read_bait_model L = int(l[1]) IndexError: list index out of range Segmentation fault (core dumped)

The command to run this was:

python3.6 /home/user/tools/SquiggleKit/MotifSeq.py -s ./output.tsv -m ./kmer.model

I've used scrappy on both my motif of interest and also with your example from Squigglekit read the docs and both times I get the same error.

The output from scrappy squiggle using your example fasta is the following which I'm hoping is the right output for MotifSeq?

`#my_kmer_name

pos base current sd dwell

0 A -0.431606 0.380354 1.058162

1 T 1.166496 0.338997 1.447607

2 C 0.450231 0.156083 4.044586

3 G -1.232723 0.151543 5.830419

4 A -1.257596 0.212146 4.654805

5 T 1.789353 0.239968 6.895236

6 C 0.315072 0.139455 7.184886

7 G -0.477836 0.110022 8.183088

8 C 0.513699 0.117384 8.406736

9 T 0.918025 0.182820 6.356708

10 A -0.463172 0.136564 6.415285

11 T 1.280751 0.209826 7.606201

12 G -0.146407 0.107954 6.591394

13 C 0.483716 0.102067 7.065899

14 T 0.864263 0.165668 7.642580

15 A -0.401214 0.111559 8.543694

16 G -0.268080 0.108424 9.368885

17 C 0.405020 0.162891 8.274393

18 A -0.954562 0.178741 7.976818

19 T 0.782907 0.137494 8.567830

20 T 0.708146 0.162590 8.998590

21 A 0.187392 0.135081 9.264595

22 C 0.513184 0.291414 17.157631

23 G -0.532910 0.667264 14.425996`

(Edited the above to put a line of whitespace inbetween each row for readability's sake, turns into a paragraph otherwise, also attached an actual copy, real one doesn't include the .txt) adapter.model.txt

[Psy-Fer]

Hello again,

Do a quick look at -h on motifseq, and you find I've built scrappie into motifseq now, so you can just parse a fasta file and it will build the model for you. Options -i and the scrappie model option.

Also, make sure you are using the latest version, 1.3.0

Let me know how that goes, I am on my phone at the moment and can give more support when back at work :)

Jamss

[690645258]

Just tested it and is running nicely with the included scrappie!

Think I must have missed that option since I'd just been relying on the SquiggleKit docs page and looks like that might have not have gotten updated with that change relevant page.

Thanks again for the prompt help!

[Psy-Fer]

Great!

yea, I will update the docs and more of the code when I get a chance. I've been busy with another project that has taken me away from this one, but always happy to give quick support when needed.

Closing this ticket.