Fastquery mode=1 not working

[harisankarsadasivan]

I'm trying to align a small lambda raw signal to a lambda genomic reference (48Kbp) and it does not seem to work with m=1. Pls find all logs below. The signal is from your drive lambda dataset and reference is downloaded from online. it is a 2-line fasta file. genome2sig.result also seems to have valid numbers.

RAw signal: Lambda_data/Lambda_3000_signal/fa10a452-c965-406e-99b4-9f41e30d8b39.signal (from your dataset)
reference genome: https://www.ncbi.nlm.nih.gov/nuccore/J02459.1?report=fasta

./sat-query -i ../../ref.fa -p ../../cwSDTWnano_Dataset_lite/Lambda_data/Lambda_3000_signal/f1ada8b7-8933-477e-aed7-fccc776bc480.signal -m 1 -o out

output:
Transform genomes to signal sequence...[Beginning] 2020/10/13 Tue 12:20:25
48502 genomes are readed.
Transform genomes to signal sequence...[Finished] 2020/10/13 Tue 12:20:26 (time elapse: 140ms)
Short reads inquiry...[Beginning] 2020/10/13 Tue 12:20:26
61255 signals are readed.
Fast inquiry...[Beginning] 2020/10/13 Tue 12:20:26
Feedback-->[-1 : -1] in the raw signal
Fast inquiry...[Finished] 2020/10/13 Tue 12:20:26 (time elapse: 110ms)
Short reads inquiry...[Finished] 2020/10/13 Tue 12:20:26 (time elapse: 140ms)

contents of output file:
-1 -1 | 1.92252e-318 2.42844e-318 | 2.61057e-318 2.61057e-318 diff: 0

[harisankarsadasivan]

I debugged a bit further and saw that I was getting 3 seeds, however, legality check was failing at the first out of 3 checks made seed_align[i].back().second < seed_align[i-1].back().second || seed_align[i][0].second < seed_align[i-1][0].second.
any hints on how to fix this will be useful.

Tried: tried increasing L to 192, 256 and also s=8,9,10. The same error happens. This should mean that the seed hits are not in order. Why would this be? Am I using the correct reference genome? What should I do to fix this? I can also be contacted at hariss@umich.edu. Looking forward to having this fixed.

I can see from your running_command file that you are trying out k=1 with default 128bp. Does k>1 not work?

[icthrm]

according to your output, you searched a 48502 bp ATCG genome on a 61255 long signal (about 61255/8 bp genome). Therefore, there will be definitely no match signal. Under this condition, we will output -1. harisankarsadasivan <notifications@github.com> 于2020年10月14日周三 上午12:27写道：

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I'm trying to align a small lambda raw signal to a lambda genomic reference (48Kbp) and it does not seem to work. Pls find all logs below. ./sat-query -i ../../ref.fa -p ../../cwSDTWnano_Dataset_lite/Lambda_data/Lambda_3000_signal/f1ada8b7-8933-477e-aed7-fccc776bc480.signal -m 1 -o out output: Transform genomes to signal sequence...[Beginning] 2020/10/13 Tue 12:20:25 48502 genomes are readed. Transform genomes to signal sequence...[Finished] 2020/10/13 Tue 12:20:26 (time elapse: 140ms) Short reads inquiry...[Beginning] 2020/10/13 Tue 12:20:26 61255 signals are readed. Fast inquiry...[Beginning] 2020/10/13 Tue 12:20:26 Feedback-->[-1 : -1] in the raw signal Fast inquiry...[Finished] 2020/10/13 Tue 12:20:26 (time elapse: 110ms) Short reads inquiry...[Finished] 2020/10/13 Tue 12:20:26 (time elapse: 140ms) contents of output file: -1 -1 | 1.92252e-318 2.42844e-318 | 2.61057e-318 2.61057e-318 diff: 0 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB2IPE6DHEFSBNN6DFNNJ6DSKR5VPANCNFSM4SPGWHBA> .

[harisankarsadasivan]

@icthrm I see, how do I search the other way around? My intention is to search for the raw nanopore signal in the bigger 48502bp long genome.

[harisankarsadasivan]

@icthrm , So it seems you dont support searching for raw nanopore signal on the bigger genome. I tried swapping reference and operated peer to make this happen and seems the seeds dont pass linear regression. Hence, I do not think cwdsdwt works well for the purpose stated. Let me know otherwise.